EDIT, since I solved my problem. I will leave my original post below as a reference to anyone who may be in the same boat.
Here is what I did:
Seven of my game folders displayed 100% locally but I got sync errors online. I used the "delete" function through CFW to remove the local trophy folders for all seven games. Then I reloaded each game until the title screen, quit, and saw new 0% trophy folders for each game. I used FTP to move those seven folders to my PC, then used PS3TIG to edit the time stamps for the trophies, while being sure to enter the days/times for the trophies that I had already earned for each game (only one game had a genuine 0% since it was pretty bad and I had long given up playing it).
Word to the wise: be sure to keep copies of the original trophy folders in case you mess up in PS3TIG, but ALSO be sure to keep copies of the modded folders that have the new date/time stamps on them just in case Brute Force hiccups, which it did for me. It would freeze while I was trying to rebuild and re-encrypt the seven folders, so I finally just did each one manually one at a time. When all of this was finally done, I deleted the clean 0% folders from my PS3, used FTP to load the new 100% folders, and finally rebuilt the database.
Boom! All seven folders showed local 100%, then I used PSN Patch and synced online. Trophies are all sorted and everything is good to go!
The process took a while, but in the end it was worth it. Hopefully this info will serve as a sort of tutorial if anyone else needs it.
TL : DR version of what I did:
1. Delete synced trophy folder(s) through CFW
2. Reload game (to title screen) to get a new, clean 0% trophy folder
3. Copy clean, 0% folder via FTP to PC
4. Create new time stamps with PS3TIG
5. Use Brute Force to rebuild and re-encrypt trophy folder
6. Delete clean, 0% trophy folder from PS3
7. Copy 100% folder via FTP to PS3
8. Rebuild database
9. ?
10. Profit
Originally posted by another user
Also, if you can't find the trophy folder for a game but YOU have the game, you can still hack them. What I did was log into another account, load the trophies there, and proceed to edit them and use Bruteforce afterwards (also never forget to rebuild the database).
Sorry to be that guy, but can you please clarify how you did this? I have a handful of games that didn't recognize the 100% I boosted with PS3TiG, but most of the folders I used worked just fine (all of them came from my own profile but were at various states of legit completion). When I view all of the trophies offline, I can see 100% on all of them, but when I view online I can see a handful that didn't sync properly.
Is this a matter of using a CFW tool like Multiman to copy the entire trophy folder from my main profile via USB over to the new profile that I created last night? If that's what I need to do, then will the offline 100% show up for all of the games like they do on my main profile? Is the next step to re-back up the second account's trophy folder to USB and use Brute Force to re-sign over to my main profile?
I would appreciate any help and guidance that this receives. Thanks in advance!