Upgrading to 0.99 from a pre 0.99 release:

I changed the .pc file format.
J-Pilot now uses .pc3 files to store desktop records.

This was necessary to make it machine byte order independent.  The .pc3
files should now work on NFS mounted drives from different architectures and
you can ftp them to other machines with different byte orders, etc.

This may make plugins need to be recompiled, or maybe changed, but I feel
this change had to be made before version 1.0.

You should sync before upgrading to 0.99 from an earlier version.
However if you can't or forgot, then you should backup and then run
jpilot-upgrade-99 and it will convert the .pc files to .pc3 files.