The original cavity for filling the flashing seal was wide but not deep,
so
I made it deeper with angle grinder and filled with mortar. The slot was
too
wide anyway for sightly or economical use of silicone. So now I'm after
some silicone based product that can be absorbed by the mortar. I was
under
the impression there was one?

I can't see a surface coating being a long term solution.

Did the mortar not have enough cement in it? It should be pretty waterproof
itself.

Christian.