I'm in process of testing post-conversion file set. The intial conversion was a snap, just open all the files and let it run. I've discovered one issue, though, with file references that will disrupt your TO's and relationships if not taken care of before conversion.
IF you have any file references specified as Filemaker Network format, fmnet:/IPHost/filename AND you change the host name in process of setting up conversion, none of these file references will work.
Majority of my file references are defined simply by local file, I'm happy to say. Only 28 file reference issues across legacy solution with 50+ files and hundreds of file references.
If you don't change the host name, of course, there is no issue. However, I'm sure like many of you, we have our current system at host still running, and are testing 12 server install on new beta host. So on actual launch, we would stop the FM11 server host anyway to convert the files, at which point we can rename the FM12 to the legacy IPdomain name and that should solve the problem for when we open the converted solution.
Alternatively, if you want to preserve ability to launch at new domain name (which is good effort in and of itself), you just need to excise all the "fmnet" file references in your system.