With regard to the Conwy Valley we probably do need to choose between rebuilding some parts to be more resistant to flooding (though some bits of such work were done last time some washed away, and indeed the following time it didn't wash away, probably as a result) and closing it[1]. Doing the work probably wouldn't be that expensive in the great scheme of railway spending, it's only a single-track low-speed diesel branch line, not HS2.
[1] But if it was closed, it should in my book, other than possibly the tunnel, be turned into a cycleway - so money would need to be spent either way. The flood issue in the case would be avoided by bringing some sections down to ground level so the water can just wash over the top - the washaway issues are occurring on elevated sections on the floodplain.