I’ve run into this issue with obsidian, but for whatever reason I haven’t had any issues with keepassdx.

When opening an existing keepass vault, on the left there’s an “Open From” pullout menu. You should be able to select your nextcloud from there. Then find your keepass file and it’ll just work.

I don’t know why, but obsidian doesn’t have the same file picker. There’s no “open from” menu. So you just have to drill into the filesystem, find the folder nextcloud is using, and choose your notes vault you’ve sync’ed in there. And for whatever reason, that seems to be the method that breaks Two-Way Sync.