According to the manuals Forms configuration should be edited using either the Enterprise Manager console or through WLST commands in 12c and not by editing the files on the server.
The rationale behind this is that these files are maintained by the Domain Administration server, so any change made later using EM or WLST will overwrite any manual changes.
However, editing many settings, especially when having a load-balanced system with multiple nodes, is a tedious and error prone task, so it would be better to still be able to edit the files manually.
Also, when migrating Forms configuration (in-place upgrades are hardly ever the way to go, e.g. when upgrading from 11g to 12c it is often desired at the same time to switch from 32-bit to 64-bit OS or from Windows to Linux) it is desirable to be able to just copy (parts of) config files instead of editing through EM.
This said, it is of course no problem to edit the originals of the configuration files that reside on the Admin server node. These will be replicated by NodeManager to the other nodes. The only thing to remember is to bring all nodes down before making the edits. Upon restart all changes will be replicated to all nodes. In the case you have a multiple node installation then this way it is much easier to make changes for one node and just copy all the changes to the respective files of the other nodes.
We used this concept in 11g to first configure one node and test everything, and then replicate it to other nodes.
Finally the question:
The only problem in 11g are custom environment files (.env files). These are not edits, but additions, and EM has to be aware of these extra files. For this purpose the file user_mbeans.xml was present in 11g. It registered all the .env files. So just copying that file to other nodes solved the problem. In 12c, however, no such file is present. So how can we configure this in 12c?