After setting up paperless and Immich I struggled with this as well. I had a structure before an was very attached to it. But both, like mentioned below, will organize files in their own way. There are ways to keep things like you had them, export them, whatever. But I deemed it to be not worth the effort.
It took me some time, but I just accepted whatever these do. In particular since I really like those two services mentioned. Data is accessed through them, and that's it for now. I backup everything through proxmox mechanisms, which is way more convenient then messing with the data in any way.
Should I want to migrate, I can always cobble together a migration script that pulls my data in ways I like.
I only handle "official" stuff with it. So invoices, some personal documents and the likes. PDF and image files, that's it.
What do you mean by "change"? Never noticed anything.
I still go through the effort of naming my files properly before uploading. So I could just take all the files and still kind of work with them (outside of paperless). But even that is overkill I guess...