No I didn't follow your wording...
It was not clear whether you were referring to songs being added/deleted from the device...or the playlist. The manner in which you worded your posting it sounded (to me) as if you were suddenly and magically editing songs files.
As for song adds/deletes from the library on the device: generally manufacturers GET IT when a song is removed. That device with a playlist that refers to that song--if not modified--will simply ignore the song when said playlist is being used. That playlist will not refer to a "different" track.
As for your need to find a device that allows for an auto pause after each song: that device may not exist despite how curt you are with me. I can certainly sympathize over the hassle of having to create individual "playlists" for each and every song file you use, but that's something that you might be up against given the actual devices that are currently available. Yet I don't see any point in getting bent out of shape over it either, since it's not up to any of us on what functions are included or not included by the MP3 device maker.
Bob's suggestion is probably going to be the best way of achieving what you need in a portable player, assuming of course such an app exists. If not there, then perhaps there's a app/program available for a laptop/netbook that could fulfill the same role...again, if such an app exists.