@akatarmo Thank you for the comprehensive and clear description of the problem.
Please send to us a copy of Insync logs and “dbs” from your machine to support@insynchq.com. The “dbs” folder is located beside the log files. Create the copy of the “dbs” folder, compress it and then send it to us (upload it to Google Drive and send the share link if it is too big to email).
In the email kindly mention the path of an example file/folder which is not uploading.
Thanks