Thanks for the suggestion - I tried removing the file from the extras folder. It took about half an hour but it blackscreened (music playing) passing between the gate house leading to Goldenrod City.
Tried every bootstrap release 0.28.0 to 0.35.1 since the weekend, always leading to a crash. The odd part is I'd had no issues for 25 hours of previous play on N2DS, mostly on bootstrap 0.28.1, but also on various releases between, until I upgraded to 0.35.1. After this I can't stop the freezing even by regressing (I even completely wiped the _nds folder and started again from an earlier version). Just to reiterate, on DSi XL with CFW, freezing was regular even on the releases I found to be stable on N2DS. I've been using the same HeartGold dump for a long time - made with Godmode9. I only use good quality Sandisk MicroSD cards and read/write speeds don't seem to be an issue.