I've got a timber framed property where the timber is failing.

As long as you have rubbed down using 80 to 120 grit you should be fine but may be you should test first ,the only issue I could see is epoxy reacting with contaminated paint,I use epoxy on rotten wood to harden the wood the fill and paint,the problem at the moment is ici and all manufactures are struggling to find a formula to comply to eu leg,regarding paint that why ther paint is crap,when it becomes water based you might as well use emulsion.good luck.