No, the two systems have the same file format. The only known issue between the two is that model notes draw differently in the two systems. This is a function of the different DSL framework versions used in the two systems. I doubt the file will reload in the 05 environment either.
We've seen this a couple of times, but haven't managed to get a reliable repro case. The fix is to open the file in the xml editor. To fix it:
Open the .orm file in the xml editor. Use the File/Open/File... dialog. Instead of clicking the 'Open' button, click the down arrow on the right edge of the Open button, select 'Open With...', and choose 'XML Editor' from the list.
Find the missing identifier. If you open the Error List (View\Error List), then you will see the missing id listed in the error list. This is most likely in a ref="_IDVALUE" attribute in the file.
Copy the element so you can show it to me.
Delete the entire element that contains the attribute
Save the file
The file should now open cleanly in the ORM Designer.
On a side note, I generally turn on the 'Miscellaneous Files' project in the solution explorer. To do this, open the Tools/Options dialog and select the Environment/Documents page. You'll see a 'Show Miscellaneous files in Solution Explorer' option. Check it, then set the '## items save in the Miscellaneous files project' to something other than 0. Now, if a file fails to open, you will be able to see it in the Solution Explorer. Right click the file and and choose 'Open With...' here.
Hopefully we can track what's doing this, I've seen it 3 or 4 times, which means the chances of you hitting it again are slim. I don't know if that is any consolation, but it's the best I can do until we get a reproducible set of actions.