@cloggy: Just create two separate libraries for 0.6 and 0.5. Then locate the file global.py (should be somewhere under ~/Library/Preferences) and edit the library_path setting in that file to point to whichever library is appropriate for the current version of calibre. Then when you start calibre, that library will be used.
As for the MOBI conversion bugs, one large source of bugs has been fixed for te next beta, so try it out.
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