Perhaps editing the flags using FlagsEditorEX? I find the bulk tag apply options in PKHex are far too generalized, and often reactivate a lot of trainers I don't want it to. FlagsEditorEX still has some limitations but its still a lot easier and faster than doing it by hand in PKHex one at a time. I wish I could just import specific tag lists from file or type them into a box in the flag researcher format. I'd absolutely go through the work of compiling per-route trainer flag lists if I could reapply them in one action that way.
Technically the bulk edit options in FlagsEditorEX are also too generalized, but at least it makes most trainer flags human-readable so you can do it by hand faster.
Same goes for overworld/hidden items on routes. I've long wanted the capability to just import a list of flags and put everything back (non story related, no key items or TMs in games with unlimited use)
