please supply more info. so we can give you proper suggestions. generally felt paper is okay for a short period as a way to keep rain water off the wood plywood roof decking until the shingles can get installed. Give a little more info. on your roof slope design,,,, sounds like it has an area of low pitch or is it no pitch??
It is never a good idea to put roofing material on a wet wood roof deck. but should understand why it got wet and fix that too before proceeding. the deck wood may be damged and maybe should be replaced first too. LJ