yes an option to 0byte the files would be nice but you can relink files so you do not delete them. (it is like dummys for .pmf files so you can only see one file but they are all there) I only delete the update folder.
I tried to rip Def Jam Fight For NY: The Takeover with UMDgen 3.5 and it did not work.(it only worked with VcdromX) I will try to rip it with UMDgen 3.2 and see if it works.
Edit: Today I tried to leave the UPDATE folder in the Def Jam Fight For NY game and used UMDgen 3.5 and 3.2 (did not work) the game did not start. It only worked with VcdromX for me.
After Def Jam Fight For NY did not work like that I tryed to use the LBA fix that UMDgen 3.5 has and it did not work. The same thing with Kazuo(JP) the LBA fix did not work (it only worked with VcdromX) This are the only 2 games that do now work in UMDgen for me.