Some files do not synchronize! Even if they should. Maybe related to Read only library.

I have setup a library in SharePoint Online, on our Intranett.

Everyone has read access to the library.

The library contains folders and files, about 185 documents. The total size is about 115 MB.

The files are templates for Word, Excel and PowerPoint. They are all saved in the lastest office file formats.

I have setup Onedrive to sync this library on all computers and chosen "Always keep on this device".

Then I have setup Office to use the synced library as the Company Templates.

When I add or change files in the library, all computers get the latest version of the templates.

This has been working very fine and people loves it.

The joy lasted about 3 months. A few weeks ago this changed and suddenly files were missing.

What happens is this:

Initial synchronization of the library get all files in SharePoint and stores them locally.

After 1 day or more, some files stops showing in the local synchronized library.

They are still in SharePoint Online.

I experience it is different files that is missing on different computers. Meaning I have not seen a pattern that there is s specific folder or file that is missing. Seems to be random.

If I stop synchronizing the library and setup sync again, then every files is back and shows up locally.

After some days, they are gone.

So what happened a few weeks ago?

I created a Flow that copies files to the library every night at 04:00.

It overwrite/replaces files if they are already there.

I do this because I need to add files from different sites and libraries across the organisation, and I very much want that process to be automatic.

My theory is that all the documents in the library needs to be synced at each user every day since I replace the files. It looks like the Onedrive sync first delete all files, then adds them. And my guess is that this process is to much for Onedrive to handle. This must be a bug?

Why should this lead to Onedrive not showing all documents in the library?

Please help since this is very frustrating for me and most important my customers. 

Please do not point me to Uservoice or Microsoft support. I know I can use them if I want and pointing me in such a direction does not help at all.