If water isn't draining anywhere then the membrane is porous whatever the cause with a little work it can be fixed. Not that it matters but was it leaking before the new piping was done? Don't try to do the job halfway it will just take longer. It's like remolding a house versus building a new house. Cement doesn't stick to rubber so just take the rocks off the top and clean them up. Remove the piping that is going through the liner, this only increases the chance of something leaking. If the original liner is really folded a lot and uneven then pull it out and line the pond with an old carpet that you can find at the curb on any given day or contact a carpet store and ask them for some used carpet. Put a new liner in and a skimmer. Either reuse your external pump (bad idea water doesn't like to be pulled) or put a new pump in your new skimmer. Reuse the stones for the edge but don't cement them, and enjoy your pond for the next quarter of a century. Total time 2 days three at most. Cost much less than doing the job with gunite or having to do it again after coating it with something else that doesn't work.
