If I delete the Undertale file in Steamapps, will it delete the soundtrack as well?
First: It sounds odd that you'd have to delete some file(s) for this, but I'll leave this portion for others.
Since you've bought the game on Steam you can (re-)download the game and the soundtrack as often as you want. Everything is associated with your account. If you delete anything, you can open the game's properties and verify the local files to restore anything missing or modified.