HOLY S*** THE FIX FROM @SonicScientist1987 WORKED!!!!! Here's the tutorial:
1-) Find the games that are missing from your GoG Galaxy Steam integration (yes you have to find them manually)
2-) Download SAM (Steam Achievement Manager, you can easily find it on google)
3-) Open SAM, Steam and GoG
4-) Go to
https://steamdb.info because you need the APPID of your missing game
5-) Find the missing game on Steamdb and copy the code from the first line that says APPID
6-) On SAM put this APPID on the little search bar from above and double click the game image, a new screen will open, just close it and it will say on Steam that you played that game
7-) Now your missing game will appear on GoG
P.s: Dragon Age Awakening and F.E.A.R Extraction Point didn't work doing this, you can't even find these games using CTRL + F on GoG, it's like they were erased from GoG Steam integration database...
P.s 2:The fix worked for only a couple of minutes, the games are gone now and it's not working anymore using the SAM trick =(