Thanks for creating this mod for IWD2! :)
 
I noticed that WeiDU didn't successfully do the DECOMPILE_AND_PATCH on 40INVIS1.BCS.
 
COPY_EXISTING ~40INVIS1.bcs~ override
DECOMPILE_AND_PATCH BEGIN
REPLACE_TEXTUALLY CASE_INSENSITIVE EXACT_MATCH
~ActionOverride(Player1,MakeUnselectable(5))
ActionOverride(Player5,MakeUnselectable(5))~ ~ActionOverride(Player1,MakeUnselectable(5))
ActionOverride(Player2,MakeUnselectable(5))~
END 
 
WeiDU copied the file to the override directory, but the REPLACE_TEXTUALLY was not applied.
 
Using the weidu command line to decompile override/40INVIS1.bcs, the text 
ActionOverride(Player1,MakeUnselectable(5))
ActionOverride(Player5,MakeUnselectable(5))
was still present in the decompiled BAF. 
 
Adding the DIFFLEVL.IDS from the IWD Fixpack let WeiDU complete the DECOMPILE_AND_PATCH successfully. It appears that although IWD2 doesn't need/use DIFFLEVL.IDS, WeiDU needs it there to compile the BAF to BCS.
 
Also, the error message for 50KURTTU.dlg is happening because there is a patch block on that file before the block that replaces ~See([ENEMY], FALSE)~. WeiDU is complaining about compiling the dialog with the ~See([ENEMY], FALSE)~ trigger still there. If you move the following block below the one that replaces ~See([ENEMY], FALSE)~, it will compile without warnings:
 
COPY_EXISTING ~50KURTTU.dlg~ override
DECOMPILE_AND_PATCH BEGIN
REPLACE_TEXTUALLY CASE_INSENSITIVE EXACT_MATCH ~!Race(Protagonist, Halfing)~
~!Race(Protagonist, Halfling)~
END
EDIT: Without DIFFLEVL.IDS, NearInfinity can't decompile and search BCS files with a Difficulty() trigger. So having the fixpack add DIFFLEVL.IDS would be helpful on that regard too.
http://gibberlings3.net/forums/index.php?showtopic=27482&p=237303