I can't say anything about upgrade process on CRS125 as I don't have any. I did upgrade on RB951 which has switch chip as well and I had VLANs defined "in old way". The upgrade from 6.40 to 6.41 went smooth for me.

I guess success depends on how device is configured and if it's configured according to "best practice" (whatever that is), upgrade will go smoothly. But the only way of knowing it is by trying. I'd take one spare unit, configure it in the same manner as one of units in production, do upgrade and check the new configuration. If it's fine, swap units and proceed with another setup. If you have multiple units configured (almost) the same way, I guess you could upgrade all of them if the first one is fine.

Do remember that "cloning of configuration" should be done using config exports (review contents against device-dependant configuration, such as MAC addresses) and not using backup files (those are not portable between units of same HW type).

The upgrade made a mess of mine, but I knew it was going to as I had multiple bridges and VLANs.
Make sure your console cable works before you start! And definitely do them off-line.

I would upgrade to 6.40.8 (latest bugfix) before upgrading to new bridge. You can always contact MT support and check from which version to new version is best. You have a better bet at upgrading from latest bugfix to latest current. At least my guess is so.
As you current version contains some nasty security flaws I would hurry the upgrade to 6.40.8 and then plan upgrade to current and the new bridge.

Hello Folks!

I successfully stepwise upgraded first LAB CRS to latest long-term RoS 6.42.10. I had prepared a script in advance with the new settings, but I never had to use it.

Step 1 RoS 6.37.5 -> RoS 6.40.9 OK
Step 2 RoS 6.40.9 -> RoS 6.42.10 OK

In Step 1 we lost the builtin p2p support, no visible problems appeared.
In Step 2, master port configuration were converted to the new bridge based with hardware acceleration and some vlan settings were automatically adjusted accordingly by replacing the old master port with bridge. No visible problems appeared.

I was not on-site, but had mac-telnet contact with the device and monitored it from another switch it is connected to, I never had to use mac-telnet, it just came back after upgrading like nothing had happened and winbox was used to login after upgrade.

Now it should be said that this lab crs configuration is less complex than the production crs:es, but it yet contain OSPF and some firewall rules, all that survived.

It proves the concept, but I will not upgrade the other production CRS:es off-site so it has to wait.

Hello Folks!

I successfully stepwise upgraded first LAB CRS to latest long-term RoS 6.42.10. I had prepared a script in advance with the new settings, but I never had to use it.

Step 1 RoS 6.37.5 -> RoS 6.40.9 OK
Step 2 RoS 6.40.9 -> RoS 6.42.10 OK

In Step 1 we lost the builtin p2p support, no visible problems appeared.
In Step 2, master port configuration were converted to the new bridge based with hardware acceleration and some vlan settings were automatically adjusted accordingly by replacing the old master port with bridge. No visible problems appeared.

I was not on-site, but had mac-telnet contact with the device and monitored it from another switch it is connected to, I never had to use mac-telnet, it just came back after upgrading like nothing had happened and winbox was used to login after upgrade.

Now it should be said that this lab crs configuration is less complex than the production crs:es, but it yet contain OSPF and some firewall rules, all that survived.

It proves the concept, but I will not upgrade the other production CRS:es off-site so it has to wait.

Multiple CRS125 has now been successfully updated using the step wise upgrade, to latest long term, there was no need for any hands on or modification.