As far as I understand, you need to migrate portal (Workspace) from Windows server to Linux\docker one.
Please try to follow my steps:
First of all, your new portal must have the same component versions as the old one. For example, if old portal had Community server v.10.5, then you should install the same version on the new server.
The point is that different versions of a product may have different versions of database tables.
You can deploy docker containers with not actual versions via installation script workspace-enterprise-install.sh .
Component version parameters you can find here: Installing server version with additional script parameters - ONLYOFFICE
Example of the command: bash workspace-enterprise-install.sh -ims false -cv 11.1.0.1506 -cpv 2.9.1.369 -dv 6.3.0.11
You can find component versions here:
Community Server: Docker Hub
Control Panel: Docker Hub
Document Server: Docker Hub
When new portal installation is done, let’s start the migration process. Prepare backup file via Control Panel on the old server > change core.machinekey parameter on the new server as it is described here:Using the Control Panel backup/restore feature - ONLYOFFICE > restore backup file on the new portal.
If I misunderstood your request, please clarify it.