I used to use Dropbox for syncing between machines, and had to do the same thing a few years ago. Utterly insane that you still have to manually undelete folders one-by-one. Also insane was the crap customer support (not sure if it's better for business accounts?) - it was all forum based, and you were lucky to get a response. In this case I did get a response, saying that one of the machines hooked up to the account must have deleted the files due to a conflict (it most certainly did not, and I'd said as much in my original post).

Aside from this I had 2 other problems with Dropbox:

1. On startup, it would render my machine unusable for over 1 hour. Now, it was syncing from 5400 RPM spinning rust, but still - there are good solutions that don't require hashing every file on the drive with the crappest and slowest possible hash implementation (USN change journal, file system minifilters).

2. Despite only syncing between 2 machines, there were frequent, unexplained 'sync conflicts' that resulted in duplicate copies of file (or sometimes data loss). These conflicts were not even discoverable in the Dropbox UI - you'd only see them if you looked in the folder and say the extra 'conflict' files

Oh, and they sent me a ridiculous number of emails after cancelling my Pro account. I cancelled in March 2016, and they regularly spammed me until October 2018. Only some of the emails I received over that time included an 'unsubscribe' link, and despite using those I did get, they didn't stop the emails - pretty scummy behaviour.

So, poor product, poor customer service, and scummy tactics. Not their biggest fan...

Nowadays I use Seafile, hosted in a Docker container on a low-powered Azure VM, backed by Azure Bloc Storage. Works flawlessly, and I highly recommend it. I understand this isn't a solution for the general population, but if you're technically minded (this is HN; you are), it's really easy to setup. You can use VM-mounted disks or AWS API-compatible block storage (Azure Blob Storage isn't, but I have another container running Minio, which acts as a proxy between the Azure API and Azure Blob Storage - it was plug-and-play, just working OOTB)