I had a problem some time ago with corruption of the Replace field; this was resolved by making a fresh backup before any update and resaving; since then there's been zero issue.
I've been using BRU heavily to rename many thousand files since with no problem, and the list was upto 435 last time i looked and saved (15-07). I opened today as usual and the list has corrupted the end and truncated to 415 entries - it appears to have overwritten a few entries at the bottom with ones already in the list from earlier on. I performed the normal fix - opened a copy, and updated the corruption and saved as a new file, closed and re-opened. only this time it's truncated to 415 entries and overwritten the end entries as before.
I've just installed 4.0.9 to see if it makes any difference; but i'm wondering if the large number of entries in the list is filling a buffer somewhere and causing it to overwrite?