It's on the MS425 (my core), I don't have MS390's, I have MS225 downstream.
What I mean is that I would disable all redundant links towards given downstream switches from the MS425 perspective.
If I have a LACP connection to some downstream switch (or downstream stack) consisting of 2 ports, I would manually disable one of them and leave only one running (if I would have 5, I would disable 4 and leave one running).
So basically, what I'm doing is killing all redundancy in my network during upgrades, just in case.
And since I'm doing this only on the core switches, if something is going wrong I can easily turn the ports back on (not disabling these links on both sides).
In a perfect world, lets say you have 2 core switches, both of them having connections to all downstream switches (LACP, 2 ports, each ending up in one of the cores), then it would mean that you just need to disable all ports on one of the core switches (assuming you have them stacked, the stack you leave enabled) - that's what I'm doing more/less.
If you read the release notes for the firmwares you will see that there is a lot going on around switches creating loops during reboots on LACP ports and so on.
Its my way of preventing these since some firmware versions ago.
BTW, maybe this known issue is hitting you?
- Switches move LACP ports to an active forwarding state if configured. This can cause loops when connecting to an MS390 or other Catalyst switches unless the bundles are configured on the MS390/Catalyst switches first. All non-catalyst ports are configured in passive LACP mode so that loops do not occur between Meraki switches (always present)
Sorry for the lengthy post and repeating myself, just ask if you have any doubts 🙂
And by any means - that is not what Meraki would suggest, its only my way of working around the issues that I kinda got used to during the years.