No map decompiler creates a perfect file. They all contain errors as they "Guess" how the map was constructed.

Best to re-create with clean brushwork than to use decompiled works.

Also, I hope you're adding in brushwork to remove gaps in geometry and not just deleting the entity that leaks...

Turn off everything but world geometry (minus displacements) and that is everything that seals in the map. If you can see a lot of black on your screen then you've got major problems.

Maybe you should copy the whole map ( go in the SDK and make a huge selection block arround everything) then create a new map and past it, and now try to compile again, mabe it will help

then your decompiler has fucked up a lot of stuff. Probally have a lot of random origin points on all entities that place them way outside the map area or even off-grid completly.

Re-create from scratch or do something new. Not worth the time and effort to fix a decompiled map just to have it come out looking either the exact same as the original or worse as with most decompiled/recompiled works.