Good to know it worked okay.
The missing folders relates to the user that lost several appointments/emails after the update. I haven't directly restored the appointments/folders to that user but instead restored them to a separate test user and manually recreated the forthcoming appointments for the "production" user. So I didn't overwrite anything for the "production" user; the folders were already missing (much more detail in the ticket).
Though indeed the missing folders are not referenced in the folders.json file.
We did work with Smartermail support to try to reduce the calendar folder.json last year, and in the end we brought it down from ~140MB to ~60MB. There were indeed some appointments with large attachments we deleted. However, this calendar consists of ~3600 appointments, each weighing in at roughly 20KB (no attachments bringing it down). In the end we weren't really able to find an answer other than "have less appointments", but we had reduced it by a lot. Deleting old appointments by the thousands is not a great option because you may want to review previous appointments (like filed emails).
What was a little strange is that we have another user with ~3500 appointments whose folder.json only takes up 12MB. Their average appointment size is less than 4KB. Not sure what constitutes the 5x larger file sizes when neither appointment has an attachment.