creating custom data fields leads to errors on present custom data fields. It looks like new custom data is written in the wrong section in the plist-file because when disabling one cd-column another one disappears too (this issue has been fixed two times in 2019, i think )…
Actually only once and version 3.5 didn’t change custom metadata at all, maybe it’s a relict of custom metadata definitions dating back to earlier versions/betas? A copy of the file ~/Library/Application Support/DEVONthink 3/CustomMetadata.plist might be useful.