I'm guessing that if anyone else makes home brewed PTH PCBs you'll have had the same problem. You get your board beautifully ready with all the holes tented over, chuck it in to etch, and a few holes lose their plating because your pad alignment isn't quite good enough. You curse your favourite deity, scream WHY??? a few times, and sob quietly in the woods until you feel ready to face the awful prospect of soldering component leads on both sides of the board, and/or little bits of wire into those lost holes. Again. So I've been experimenting with filling materials to try to alleviate the problem. I recommend avoiding anything based on PVA glue, if you are trying the same!
Well, whilst cleaning up a different kind of failure with the beloved blue film, the answer struck me. See if I can dissolve a bit of film and pour it into the holes (well OK squeegee it in). Then the holes will have photoresist in them, which should become contiguous with the rest of the film when it goes through the laminator, and come off with it when stripping. I tried isopropanol first and that did the trick, so no need to try other solvents.
So far as the experiment was able to go, it worked. The caveat is that I already had some PVA based filler in there, which contained oil (to soften it), which was creeping out during cleaning and making the board greasy (resulting in the above mentioned "different kind of failure"), but was hollowed out at the tops, so was still able to be filled on top of. However the dissolved film successfully stopped the oil seepage, filled some very small holes the filler had missed, and made a (very uneven because I used my finger) coat on the board. And it turned out lovely (caveat - it would have been a lot more lovely had it not been for the serial forck ups leading up to this point! Oh well...)
So the next experiment will have to be lining freshly plated holes that haven't suffered abuse and ill conceived filling...
And yes I know you can get 75000 boards for £3 or something from your favourite board house in China. I'm not interested in that, I'm interested in the process, and time spent learning from these mistakes is time well spent, IMHO.