In theory, any clip you see at runtime could be dynamically created, by making an empty MC and drawing in whatever contents you like with the drawing API. However, if you see clips in the library that are similar to what's showing up at runtime, then it's very unlikely that that's happening.
Your first step should probably be another look through the library. Remember that instance names don't have to be the same as MC names; even if something is called "Menu Holder" in the library there might be an instance of it somewhere called "mcMenuBkg" or whatever. But the fact that you can delete stuff without changing the output is mysterious.
So, other possibilities: contents are being loaded externally, or imported via runtime sharing. If feasible, try moving your SWF to a temp directory and running it from there; that should break all loads (unless contents are loaded from a remote URL).
Or, you're looking at the wrong clips in the library. If it's a crufty project there may be unused stuff in there. Try expanding the library wide enough to see the "Use count" column, and select "update use counts" from the library menu. Anything with a count of 1 or higher is part of your FLA's stage content - either it's sitting on the main stage or it's a child of something that is. Clips with a use count of 0 may still be used if they have a linkage ID; they could be created at runtime with attachMovie()
. However, for any clip with a use count of 0 and no linkage id, it's safe to assume that it's unused, and irrelevant to what happens at runtime.
If none of that helps, the only things that come to mind are sanity checks... open up everything on the stage and every clip with a linkage id, and check for empty/invisible MCs. Check the Movie's export settings to make absolutely sure the SWF you're checking is the same one being published. And just for grins, open up the "Scenes" panel and make sure that some diabolical fiend hasn't put important content on a separate scene where no sane man would look for it.
Vague answer for a vague question. :D Hope it helps...