js 
I have updated, yet again, Studio to see if this problem had been fixed but it hasn't yet. It was broken in the previous version of Studio but worked well about 2 or 3 versions ago. The project was finished and the board has been working for several months but can't rebuild the project.
js By the way I have 3 back ups of the successfully built project, can't find the Studio version number but I can see the device pack version as being XMEGAD_DFP/1.1.52 and this WORKED.
david.prentice 
I have never used a D4. I have only used A1 and A4.
Looking at the iox124a4u.h header:
/* Compare or Capture A Interrupt Level */
typedef enum TC_CCAINTLVL_enum
{
TC_CCAINTLVL_OFF_gc = (0x00<<0), /* Interrupt Disabled */
TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */
TC_CCAINTLVL_MED_gc = (0x02<<0), /* Medium Level */
TC_CCAINTLVL_HI_gc = (0x03<<0), /* High Level */
} TC_CCAINTLVL_t;
...
/* TC0.INTCTRLB bit masks and bit positions */
#define TC0_CCAINTLVL_gm 0x03 /* Compare or Capture A Interrupt Level group mask. */
#define TC0_CCAINTLVL_gp 0 /* Compare or Capture A Interrupt Level group position. */
#define TC0_CCAINTLVL0_bm (1<<0) /* Compare or Capture A Interrupt Level bit 0 mask. */
#define TC0_CCAINTLVL0_bp 0 /* Compare or Capture A Interrupt Level bit 0 position. */
#define TC0_CCAINTLVL1_bm (1<<1) /* Compare or Capture A Interrupt Level bit 1 mask. */
#define TC0_CCAINTLVL1_bp 1 /* Compare or Capture A Interrupt Level bit 1 position. */
...This header looks logical. i.e. xxxxINTLVL_xx_gc values in an enum with specific defines for xxxxINTLVLxx_bm bitmasks.
How are you using symbols like TC_TC0_CCAINTLVL_LO_gc ?
I suspect that your earlier "working version" had inconsistent header files.
But most importantly, please click on the errors. And paste the offending lines from main.c and on.c
David.
clawson 
Your symbol is surely misnamed?
D:\atmel_avr\avr8-gnu-toolchain-win32_x86\avr\include\avr>grep CCAINTLVL_LO_gc iox128d4*.h
TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */
So there is a TC_CAINTLVL_LO_gc but no version with "TC0" in the name (presumably so that the same can be used for multiple TCn ?). It's not just the 128D4, seems fairly consistent:
D:\atmel_avr\avr8-gnu-toolchain-win32_x86\avr\include\avr>grep CCAINTLVL_LO_gc iox*.h iox128a1.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128a1u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128a3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128a3u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128a4u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128b1.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128b3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox128d4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16a4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16a4u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16c4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16d4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16e5.h: TC45_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox16e5.h: TC45_LCCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox192a3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox192a3u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox192c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox192d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256a3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256a3b.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256a3bu.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256a3u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox256d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32a4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32a4u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32c4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32d4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32e5.h: TC45_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox32e5.h: TC45_LCCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox384c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox384d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64a1.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64a1u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64a3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64a3u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64a4u.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64b1.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64b3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64c3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64d3.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox64d4.h: TC_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox8e5.h: TC45_CCAINTLVL_LO_gc = (0x01<<0), /* Low Level */ iox8e5.h: TC45_LCCAINTLVL_LO_gc = (0x01<<0), /* Low Level */
E5s have a variant with "TC45" in the name though.
@david.prentice wrote:
I suspect that your earlier "working version" had inconsistent header files.
Or Atmel decided to drop the TC0/TC1 designation from the header files as there is no difference between them.
This is the trouble with tools which keep updating themselves as you go along - it makes configuration control an absolute nightmare!!
meolsen 
<sigh>... if only there was a device pack system that allowed you to lock your project to an older version of the headers....</sigh>
js Is there such a system? And don't the device pack being updated delete the old packs?
And for the doubting Thomases that may think it never compiled or I used some wrong names 
TCC0_INTCTRLB &= ~ (TC_TC0_CCAINTLVL_LO_gc); // Interrupt off
b708: e7 e0 ldi r30, 0x07 ; 7
b70a: f8 e0 ldi r31, 0x08 ; 8
b70c: 80 81 ld r24, Z
b70e: 8e 7f andi r24, 0xFE ; 254
b710: 80 83 st Z, r24
TCC0_INTCTRLB |= (TC_TC0_CCAINTLVL_LO_gc); // Timer interrupt on
d5b2: 80 91 07 08 lds r24, 0x0807 ; 0x800807 <__TEXT_REGION_LENGTH__+0x700807>
d5b6: 81 60 ori r24, 0x01 ; 1
d5b8: 80 93 07 08 sts 0x0807, r24 ; 0x800807 <__TEXT_REGION_LENGTH__+0x700807>
TCC0_INTCTRLB |= TC_TC0_CCAINTLVL_LO_gc; // Low level priority
d9e8: 80 91 07 08 lds r24, 0x0807 ; 0x800807 <__TEXT_REGION_LENGTH__+0x700807>
d9ec: 81 60 ori r24, 0x01 ; 1
d9ee: 80 93 07 08 sts 0x0807, r24 ; 0x800807 <__TEXT_REGION_LENGTH__+0x700807>
// Timer4 compare tick every 5ms from 32MHz
TCC0_CTRLA = TC_TC1_CLKSEL_DIV64_gc; // clk/64
d9d6: 85 e0 ldi r24, 0x05 ; 5
d9d8: 80 93 00 08 sts 0x0800, r24 ; 0x800800 <__TEXT_REGION_LENGTH__+0x700800>
meolsen No, old packs are not necessarily deleted. But if you open a project with a version that you don't have locally then studio should offer to download it for you...
js I found where to change the device pack and post a screen shot for others.
however there are no older device packs but just the current one and the one that worked correctly (XMEGAD_DFP/1.1.52) is NOT on the list of available DPs.
meolsen Only local ones. Download the one you need and it will become available in the project list.
js Yes, but where do I download it from? It's not on the list of available DPs (XMEGAD_DFP/1.1.52), it jumps from 1.0.32 to 1.1.57 and then the current one.
meolsen Then download 1.0.32 and see if it works...
js Neither 1.0.32, 1.1.57 or 1.163 work. I may have the working version on my laptop, I think I still have the old AS7 on it.
js Found XMEGAD_DFP/1.1.52 on my laptop and copied the whole folder across but it is not visible in the drop-down menu as the pack is not "installed".
HOWEVER!! By just having that folder with the others in the device pack folder fixes the problem even compiling with 1.163, I removed the folder from the device pack folder and it failed with all 3 installed device packs, put it back and all is well with all 3.
So Studio must just search the other packs for definition even though not selectable??
meolsen Hmmm, no... To make it visible you need to reindex (it's in a menu in the Device Pack Manager). However the project should not look inside it before it's selected...
js you need to reindex (it's in a menu in the Device Pack Manager)
Can't see it.
Anyway it works now regardless of what fixes it. 
I'm updating my laptop to see if the old device packs get deleted. I have saved that device pack elsewhere in case I need it.
EDIT rebuilt using 1.1.63 but as you can see both 1.1.52 and 1.1.63 are being included even though 1.1.52 does not officially exist except that the folder has been copied into the DP folder.