I updated my 5.8 X86 router and I had two ethernet cards, ether1 and ether2. After the reboot, my cards were gone and the were replaced by ether3 and ether4. That destroys the configuration and if this a complex one, it makes difficult to go back up. Please fix it and send me a link for 5.12.

I encountered a similar issue when upgrading from 5.6 to 5.9 and ended up with on a 493ah with ether 11,12,13…. Instead of ether 1,2,3…. But I have now a procedure which I follow before upgrading
(1) Only upgrade at a convenient time so in the worst case scenario be able to travel to remote site,
(2) Do a backup of the router ,from terminal export file=backup
(3) Save a copy to the desktop
(4) Upload the upgrade files and check the transfer was successful and check file sizes
(5) Check you have mac-telnet access to the router
(6) Upgrade
(7) If the upgrade resulted in a issue like the one you posted then mac-telnet in and from terminal import file=backup ( or import hit return key then tab key highlight and copy file (in my example) called backup and paste, this will restore and all the ether ports are correctly labelled.
I hope this will be of help

The update should be transparent. This is a bug and Mikrotik should address it soon.

I had the same problem with device naming on X86 after upgrading to 5.11

I have this problem on all of my routers. It should be fixed in 5.9. But if you upgrade from earlier version, there could be setup messed up. Just try to reboote device, don't change enything. Everything should revert to normal.