I haven’t had to do major VFX projects yet so pardon my theorycrafting here:
If your VFX guys preserved reel and or timecode, “reconform from folders” should work, if you import your VFX into a separate folder.
If VFX files came back with all new TC, I imagine you might have to cut them in the first time, but all subsequent versions should be reconformable, provided VFX keeps their own outputs with consistent TC.