Thats what an employe now is doing, open files and copy paste from onlyoffice to recreate them in local libreoffice. Surprisingly the database content within onlyoffice is quite resistable. 
I uninstalled onlyoffice app in nextcloud and reinstalled it, and the newest versions of files are still there.
I had suggested to my boss to work only on the files online and do a final export to pdf, but aparently there are docx files with embeded documents and it could be that onlyoffice has a problem with those.
By the way as much as I would like to try if the ajax job does it’s thing, I doubt it would work as in console as root I did issue occ documentserver:flush But that did not bring the file modifications from database to the filesystem.