So I ran the filter with FCOM base and KA active.
I did not see anything that jumped out as game breaking, but I admit I don't have the eyes of Arthmoor.
A lot of things like changes to stats on NPCs given by OOO altered again by KA.
I saw at least one NPC misnamed by OOO and corrected by KA.
A container that OOO trapped and that KA reverted to vanilla.
Googlepox - have you seen http://www.uesp.net/wiki/Tes4Mod:FCOM#K_--_KD_Circlets_OOO_Optimized.2C_Kingdom_of_Almar.2C_Kvatch_Aftermath.2C_Kvatch_Rebuilt. I quote (without links):
Kvatch Aftermath -- older versions suffer from lots of pathgrid conflicts with other mods, including OOO, but this issue has largely been resolved in KA 6.6. Most of the remaining conflicts with FCOM can be fixed by using the FCOM patch included in Kvatch Aftermath 6.3 Cleaned and Fixed. The patch will work with KA 6.6 as well, but 6.6 does not include all of the "Cleaned and Fixed" elements from ElminsterEU. If KA 6.6 causes conflicts, you can use the C&F 6.3 version, but you will miss fixes for KA elements added by Giskard after 6.3's release. It's currently unknown whether all of the other issues addressed in the C&F 6.3 version have been resolved in 6.6.
Again the UESP site has links, but the link to the FCOM patch is gone. I don't have it in my archive.