I would recommend you avoid the syncing all together!
The danger is this - firstly the sync can break as you've mentioned and you can end up with users with lots of files that dont match whats in Sharepoint and that can take days to fix, but worse people will all have those files on their laptop and if any one of them casually thinks 'oh Im running out of diskspace' and deletes them, assuming those are only local copies, well theyll get deleted off the cloud and off every persons device across the company.
So that doesnt mean, dont use Onedrive - but do this:
Use Onedrive to have them sync only their personal files from Sharepoint. They should already see this folder in their file explorer
Let them create Onedrive shortcuts to specific folders they may want to use on a regular basis. This creates a folder inside their Explorer personal Onedrive folder I mentioned above, and creates a folder named after the sharepoint site/library.
This is most useful for where someone needs to save things to Sharepoint that are not Office based as it is accessible via a drive path c:\ type of stuff. So for text files, powwrshell scripts that sort of thing. As long aa the staff understand the point above about not deleting it from C without ubderstanding that takes it out the cloud aa well.
Then for normal users, show them how to open documents/spreadsheets via the Edge browser or from the app directly. Thats the correct way to use Sharepoint. Every document is available via search and you can open in browser or in app.
Microsoft have some new apps you install which shows recent Sharepoint files from your desktop.
You can also go to the Onedrive web page and browse any document, or any files shared with you.
So what you do is STOP people thinking about explorer as a way to get to files.
They should think about Edge and have an Intranet and a home site, and a hub menu navigation and their default web page should already show recent sites, recent documents, pinned doc
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