Same goes for me, we resolved this issue several times by resetting the flex flash controller.
You just have to be patient: after the reset it takes some minutes after the error disappears.
Having similar issue with (UCSB-B200-M4) FlexFlash error below: will resetting wipe out the contents of SDCARD? Will the ESXi Host bootup fine after reset?
Reseting the Controller is disruptive as the server looses the connection to the SD cards.
But it will not erase the content of the cards. If you want to delete the cards you have to choose "Format SD Cards".
Error Invalid Size typically indicates a problem with the SD card themselves.
If you were getting a "flexflash controller unresponsive" then a reset would likely resolve this.
I have also seen this message when the two SD cards being used are not identical. (Different size, etc). The platform requires that the two cards be identical.
We have 2 SD cards setup as RAID1, but that server is only showing 1 now, and it's marked as an "Unpaired primary" that will not boot ESXi? Is having 2 cards pointless for HA/redundancy?
Having two cards is necessary for redundancy, yes. It sounds like the OS may have been corrupted or lost after the upgrade. If the card would have failed during operation, the OS would remain on a single card.
When you attempt to boot the server, do you get an error? Does ESXi display anything or do you get "no boot device found"?
The most effective use of time would to be just re-install ESXi and re-configure the management settings. If you would like to try and recover, I would boot an ESXi Installer ISO and choose to "upgrade" and see if the boot partition is still available. If not, it may have been lost/corrupted during an upgrade/when the card failed.