We have a lot of different RB's (age, type) with various versions 2.9.x. Before v3, we were normally upgrading as soon as this forum indicated that there were no major problems. With V3, it is another situation.
Many upgrade attempts from 2.9.x to 3.x has resulted in broken links, climbing, unbootable boards etc. Generally very unpredictable...
We have found one way to succeed every time. It is a little more complicated than normally, but it works 100 %. The requirement is a connection to ether1 on the board to be upgraded - either indirectly from a neighbor in the same tower, or directly with a pc at the end of the cable. The required steps are: 1) Reboot the RB, 2) make a backup and copy it to your pc, 3) make a "system reset", 4) copy the new firmware to the board, boot and make a "sys rou upg" and boot again, 5) Restore the backup.
Our conclusion is, that v3 is not always able to make the conversion of the custom setup from v2 on-the-fly. Luckily, the back-up/restore works well !
Please Mikrotik, fix the broken software !