License issues are not related at all with a multi server installation. You are right in thinking that revocation is not possible as your license is now invalid. You cannot revoke an invalid license. You can only revoke a valid one, and the moment you moved a license file into another server you invalidated it. So, you must run /usr/local/fop2/fop2_server --revoke on the original server the license was issues... and you should check that the license is in fact correct with /usr/local/fop2/fop2_server --test. Only if the test is successful then the --revoke will work. Now, once revoked, you will be able to run /usr/local/fop2/fop2_server --register on the new server directly, and it will retrieve a new license file directly.
As for configurations. I do not know what you did in your current setup/configuration, so I cannot answer properly.
FOP2 configuration can be static text files, or you can run a script that outputs valid configuration data and use that as config. The newer FOP2 version includes a FOP2 Manager that will store every configuration in MySQL, and then it will use a script to retrieve that and generate valid fop2 user and buttons data. So, the fop2.cfg file has only this: #exec autoconfig-users.sh . That script will read MySQL fop2 tables to generate user,groups and plugins data. Then it will load the autobuttons.cfg file that will in its place execute the script autoconfig-buttons.sh, that will produce the buttons configuration data (also by querying mysql).
The FOP2 Manager detects your backend and will query that backend via available means to populate fop2 tables with data. In FreePBX it queries some tables to get configuration. In some other backends it reads some static files, in other it could be mixed between db and static files.
You can very well remove that #exec line and write static user=xxxx lines, or write your own scripts, or whatever. FOP2 and the FOP2 Manger won't create FOP2 users automatically if you add an extension in FreePBX, that is a design choice. You can manipulate fop2 tables by other means if you want, but it is not really recommended (unless you want to auto create users). But be advised that user tables are several and they are interrelated. Look at the mysql query in autoconfig-users.sh to have an idea on how things are done sql wise.
Best regards,