I have exactly the same problem, I posted a separate report as requested by Nextcloud as it went through the update process, and like most of you here, I have had no one come back and explain what seems to be the problem.
I did find this on Git though:
Hi @AndreasB92 ,
I had the exact same issue. I resolved it by running the following query against my database (MariaDB):
DROP INDEX share_id_index ON oc_onlyoffice_permissions;
This query, drops the index for table oc_onlyoffice_permissions
. Afterwards the migration runs through and everything seems to work.
Hope that helps.