Thats bad.
I sometimes read this but i never got those problems. Badly i´m also no programmer and not udnerstand the Mobiflight Scripting myself. Just Sebastian do this.
My experience in the past was always to recommend at first to "clean" problematic Boards.... Mostly this helps in the past.
I know this is not a solution as you expect and not solve the basic issue ....NUT if it solve the problem temporary for you may its a good hint.
In your case it looks Board1 is problematic maby ( Cause here Double Device is occure) .... So do the workflow for Board1 also ( Clear EEPRO and flash new firmware)
To protect you of creating all devices new i recommend to SAVE the current Settings of both Boards in a MFMC File each.
MABY the problem is also in your USB Drivers of Computer but i don´t think so. Another issue spot can be ADMIN Mode.... If possible try to run Maobiflight ALWAYS as Admin if you not do it already. ( NOTE you then also must run Your Sim in ADMIN Mode .... Else you get in trouble again)
About last question: NO i don´t know to test a Mega directly and normaly thats not needed. Megas got broke verry rarely... and if yes they most completly broke by a high voltage or so..... So you smell it if its broke or see a little smoke coming out of it
Maby Broke Megas also completly not recognize again.... Or maby they work but just aPin is simply broke. But your reported Situation NOT looks for me as a broke mega at the moment.... Maby i´m wrong. Lets test this by EEPROM Clear then we can talk again !
EDIT: About Pictures.
Here In Forum you need to upload the Pictures to a Puplic Webspace (Filehoster) or to your Own Webspace if you got and jut LINK it in your Posting. Not possible to upload Pictures directly.....
Alternate is to Join us in DISCORD..... There you can send Pictures.
Email is also possible but i think not needed in this situation !