keep them in the EP
I don't like to edit the tracklist of the album, unless it's adding exclusive bonus tracks in different version at the end of the album
Keep the EP intact, unless all of the songs are on the album, then I'll delete the EP entirely. No need for a whole EP of duplicates. Unless the songs have been changed in some way. Then I'll most likely keep the EP too.
If there is a certain remix or acoustic version like Beyonce's Best Thing I Never Had Acoustic Version.. I add it as an exclusive bonus track on my iTunes
Usually I keep them how they are, unless there's only like 2 tracks that don't go onto an album. Then I'll add them on. I kept the Truth Serum EP how it is, except for Love Ballad which I deleted (I added it on in the first place).