Hmmm... Another serious bug. This one affects all 1.4 releases until now and is fixed with 1.4.3b. The effect is that flagged items are dropped out of cache like normal (unflagged) items. With this behaviour you will propably have lost all your old flagged items. Newer ones will propably not be affected.
How to verify this: Check your "Important" search folder. Sort by date and look for the oldest flagged items you can rememeber.
Workaround: If you cannot upgrade to 1.4.3b right now please set a very high feed cache size in the preferences and thereby disable the cache dropping.
Solution: upgrade to 1.4.3b
How to recover data: To be honest this is pretty hard. If you just migrated from 1.2 to 1.4 and didn't delete ~/.liferea_1.2 I'd suggest to remove ~/.liferea_1.4, thereby loosing all intermediate changes and to automatically remigrate again. This is a way to recover old important flagged items in case you value those more than the recent new items and their state changes.
If you have questions join the IRC channel (#liferea at freenode) or the mailing list. Sorry to everyone that lost flagged items this way!!!