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The ISR should keep working as long as the functionality of the interfaces in \src\SubPic\*.* remains the same. Can you poke xy about that? Porting any changes from MPC-HC in that folder to xy-vsfilter should simplify a future merge.
The only other important change missing in xy-vsfilter is x64 support.
Most of the remaining changes in MPC-HC's VSFilter are cosmetic. Like astyle code formatting. A bunch of compiler warning fixes. All stuff that could be redone if necessary after a merge/replace. There might be a couple of bug fixes that haven't been ported to xy-vsfilter yet. But making a list of those shouldn't be much of a problem when going through the SVN history. I could do that if needed.
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