Strange AI and Scenery error when "updating" the BSP

[L0d3x]

I'm just going to illustrate the problem at hand by copying an AIM conversation in here, it completely describes the problem:

L0dex: alright
L0dex: so the situation is as follows
L0dex: higuy had given me an unportaled bsp some time ago, which i had to populate and script etc
L0dex: i added some extra scenery to it, and the ai all worked fine
L0dex: now higuy gave me an updated bsp, which has been portaled
L0dex: after replacing the old bsp with the new one (and the corresponding lightmaps)
L0dex: the ai seems to be COMPLETELY invisible (except for gun effects), and they cannot die, nor does anything collide with the ai
L0dex: i also noticed that
L0dex: the extra scenery i had placed
L0dex: which should be completely disjoint with the BSPs
L0dex: this extra scenery
L0dex: is no longer here
L0dex: or it won't show up anyway
L0dex: rerunning lightmaps did not help
ShadowSpartan1: ummm
ShadowSpartan1: hmm
L0dex: do you have any idea at all what could be causing this?
ShadowSpartan1: when you open in sapien
ShadowSpartan1: what's it like
ShadowSpartan1: is teh scenery properly placed
ShadowSpartan1: as well as the AI encounters and shit
L0dex: uhm its all properly placed, same with ai firing positions, starting positions, etc
ShadowSpartan1: weird
L0dex: mhmm
ShadowSpartan1: so if u go back to original bsp, it's fine?
ShadowSpartan1: or have u even tried that
L0dex: yes it's fine then
ShadowSpartan1: wow
ShadowSpartan1: hmmm
ShadowSpartan1: I'm not sure tbqh
ShadowSpartan1 signed on at 23:27:30.
ShadowSpartan1: so it's all properly lighted and shit, which means u have the right ligthamsp tag
L0dex: yes indeed
ShadowSpartan1: idk really
ShadowSpartan1: makes non sense
ShadowSpartan1: no*
ShadowSpartan1: I would try asking on the forum

So as Shadow the wise suggested, I am here, pleading you all for help and/or ideas...

So, who knows how to solve this very odd and illogical problem

[Dwood]

Redo the ai and see what happens?

[L0d3x]

The AI encounters and stuff are still there...
And making new encounters in this scenario still results in invisible/invincible characters.

[Higuy]

Redo the ai and see what happens?

No, thats stupid, becuase its not like there messed up if you think about it.

[chrisk123999]

Is the BSP in the same exact place?

[L0d3x]

Yes it is. The only difference is that it's been portaled, that is all.

[Gwunty]

Have you tried compiling?

[L0d3x]

Yes, compiling left the same problems ingame as in sapien.