Dear Nadav,
Good day!!
Apologies for the inconvenience caused and please don’t worry, let’s work together on your concern and move towards a resolution path.
I understand your concern and since you mentioned the synced shared folders became the links to the web version of OneDrive, where re-installing the OneDrive sync client and re-connecting didn’t fix the issue, I would like to confirm whether you have cleared the OneDrive setup folder in the Windows AppData before re-installing the OneDrive sync client.
If not, I would like to suggest you try the following steps and check the outcome:
Step 1: Click on the OneDrive icon in the task bar> Help & Settings> Settings> Account> Make sure to unlink any Office 365 account connected to OneDrive sync including personal OneDrive. (please proceed with the next step if you are having trouble with step 1).
Step 2: Quit OneDrive sync client> Uninstall the OneDrive sync client (Turn off, disable, or uninstall OneDrive - Microsoft Support)
Step 3: Open the File Explorer> C drive> Users> Folder with the user profile having the problem> AppData> Local> OneDrive> Move the Cache folder to Desktop> Go back to Local folder path> Go to Microsoft folder> OneDrive> Move the setup folder to the desktop location or rename it.
Step 4: Go to the Control Panel> User Accounts> Credential Manager> Windows Credentials> Remove/Delete identities related to OneDrive.
Step 5: Restart the PC> Install the OneDrive sync client (OneDrive release notes - Microsoft Support – download and install the latest Production version)> Open the OneDrive sync client and setup your Office 365 account and shared folders to see the outcome.
If the same problem persists, we are sorry and I believe the problem should be further investigated by the related development team, where they can collect the fiddler logs while reproducing the problem and perform the further investigation.
So, I request you to connect with your IT admin of your organization (How do I find my Microsoft 365 admin? - Microsoft Support) and raise a new service request from the Microsoft 365 admin center so that the related development team will connect with you and investigate the issue further.
Reference: Get support - Microsoft 365 admin | Microsoft Learn
Note: We apologize for redirecting you to related development support team because the moderators in this community are limited with the resource for further investigation and to get a quick resolution to your problem, we requested it.
Appreciate your patience and understanding. Have a great day!!
Best Regards,
Sophia