Microsoft File Server migration in my case consisted of 3 steps:

1. Copy files (including NTFS permissions)
2. Copy shares
3. Copy quotas

Here is what to do:

Copy files using robocopy

i copied files from my old to new server using following command on the source server:

robocopy.exe .\MyRootFolder \\MyDestinationServer\driveletter$\MyRootFolder /MIR /SEC /SECFIX /W:3 /R:3 /E /ZB /COPYALL /V

To learn more about the parameters, go to this microsoft page for robocopy

Copy shares

Use regedit to export / import following key and its content:

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\LanmanServer\Shares

Copy quotas

Now this was the most complicated part as it involved some scripting. First export the quota templates from the source server:

dirquota.exe template export /file:C:\quota.xml

copy that file onto the destination server and do:

dirquota.exe quota template import /file:<path_to_xml_file>

Afterwards you have to output the specific quotas and add them with:

dirquota.exe quota add /Limit:<size_in_gb_or_mb> /SourceTemplate:<name_of_the_template> /Path:<path_to_quota_folder>

Source: https://suddhaman.blogspot.com/2020/07/file-server-migration-windows-server.html