Doom3world

I edited some single player maps in quake 4; deleted some mapobjects [entities] and recompiled it again. i took all of files that were created with the .map file and put them in there designated pak archives. i tested the edited maps within the quake 4 editor and they worked perfectly. but when i load the maps in the game, the entities i deleted are back in the map/game.
what am i doing wrong? how do i fix it?

I don't recommend modifying the stock PK4s. There's no need to given you can override assets simply by archiving them into a new PK4 with a filename that alphanumerically succeeds everything else.

My guess would be that you removed an entity that is called by a function, script or trigger and thats whats killing you just because in editor you dont see a link between entities dosnt necassarilly mean they are not linked
but again without seing the actual files in question any one that answeers is just guessing