Yes if you removed all the contents of the back up folder and then hard reset then sync all that would be restored is PIM (contacts, memos, calender, pictures). You only remove files that are recreated by the system. Remove files such as

along with the ones I listed above: caches, anyhing that says blazer, localcuslocationdb, calenderlocationdb,,,,,you know,,,all files that are not your 3rd party applications or their databases,,,)
For instance I would not remove "Megalauncher" or "flashcards" or "FlashcardsEnglish".
But do remove ALL files that are recreated such as "phone favorites".
If anything the most important file to remove is "saved preferences".
After removing these files, hard reset and sync.
Then reconfigure all your applications and enter all your registration codes. It took me about an hour and a half.
If this is unclear let me know, I'm happy to help.