Thanks for the more detailed explanation. I see what is happening now.
The fact that these files are disabled means that they are in a conflicted state (I was confused at first when you mentioned the exclamation mark, assuming that they were simply out-of-date).
In that case, there are a number of ways forward but all will involve some modifications to the engine. I wonder if you have any comments on what method you would prefer?
- Prevent submission of any files when there are conflicts present in the list. Conflicts would need to be resolved using P4V/TortoiseSVN etc.
- Default the conflicted files to ‘unchecked’ (but still disabled as they cannot be checked in without a resolve).
- Allow the check-in to fail (and allow the checkboxes to be checked/unchecked by the user), providing some useful error message.