Collections and read status are stored in explorer-3.db (table Shelves)
Bookmarks in books.db. Both are SQLite3 files.
No idea if pocketbook cloud changes any of that, but for now assume it only syncs rows between these file.
BTW, with some luck, a backup might exist.
For bookmarks, my (untested) assumptions is books.db can be transferred entirely - it keeps it's own ids for books.
Afterwards you might need to fix or 'pull-up' the bookmark ids, which can be done using Calibre's pocketbook tools plugin (standalone is in the works)... though it's not been tested for this scenario

And might not work
Collections are perhaps better recreated using the reader, or the app from the other thread.