Instances can go down, disappear or be unresponsive due to many reasons.
Go to your account settings now and export your account settings!
This file contains your subscriptions, follows, profile settings etc. It’s very easy to start over on a new instance when you have your export file.
Back it up, export it, save it, repeat occasionally.
There’s a file api you can use to interact with the file system directly. Practically, I’m not sure how much it would help, since you could only access it with permission while the website is open, and there’s no way to sync between devices, but it is hypothetically possible to write a feature that backs up your settings periodically.