OK - Path/filename length may be relevant: I moved folders to the root of the drives, renamed folders to be shorter etc. It looks like the max path length is 260 characters.

This Microsoft doc and instructions towards the end should resolve this issue for you https://learn.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=registry based on the information you have provided.

Aaaah of course. Windows 11 both supporting and not supporting something at the same time. Makes perfect sense. I was very not looking forward to trying to reduce all the paths over 259 characters as there are rather a lot of them.
I made the registry change and it found 22 more results, but couldn't send them to the recycle bin. The error came up quite small, something about the data being sent being too small. I thought I'd screenshotted it, but I don't see it on my system.
The link mentions changing the app manifest - is that relevant to dupeguru and if so, where do I find it?

That error for the recycle operation seems odd, if you get it again, can you capture it?

If it comes up again, yes. At the moment I'm just running some scans on another folder, but I can redo the export to folder A (which I'd deleted as it was finally empty) to do some tests on.

I haven't seen that error again yet but the last scan I ran found a couple of screenfuls of items, which I sent to the recycle bin. When I opened the bin to clear it out, none of those items were in there, just a couple of things I'd deleted manually yesterday.
It does seem to be the case that after running a few scans in a row without closing and reopening the app (even if I clear the cache) it will do Something Weird - but it's been something different each time.

I couldn't see anything obvious in the debug log.
This was after I'd given up on deleting all of the results at once, saved the result set, restarted the app, reloaded, and tried deleting I think about 1/10th of the list (it's deduping two exports of all my mail from two different clients which use different folder structures.)

This is all the errors I ended up with after deleting in batches.

I've had several out-of-memory crashes as well, mostly after several hours at the 'fiddling with results' stage, and when closed after such a crash, the app is still showing in task manager until I end it. It looks like what it's having a problem with is a folder which has a lot of zero-size files in it. I've been able to do the subfolders and each one has had more than 15000 of those zero-size files, so I can see why doing Many such folders would be an issue.