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I have a usb drive that I plugged in physically in my Macbook and used quite a while to backup my Mac OS X system. The backup folder was called Backups.backupdb.

Recently, I attached this to a Raspberry Pi (HFS+, journalled) and wanted to back it up again. But now it's backing up as <my_computer_name>.backupbundle. I used this tutorial to achieve that: https://alexdunn.io/posts/rpi_time_machine/ (the only difference: I used Raspbian, and had to explicitly create a samba user).

I thought Time Machine would be able to recognize that it already has my system backed up on it, but it didn't.

How do I get Time Machine to recognize that I already have my old backups on there?

Edit: there seems to be a similar question here Time Machine on a local drive, then make that drive a network drive (via Server.app) on a different computer

But it didn't give the answer, this is in part, I believe, because Catalina has a new extension (.backupbundle) and because smb is now the prefered protocol.

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I'm assuming .backupbundle is just Catalina's "special" extension for a spasebundle being used as a backup method, in that case, Time Machine saw your drive as a network drive, thus creating the sparse bundle and then backup up to it.

The reason this happens is because Time Machine can't back up to network drives, only to HFS+ drives.

You can't get it to recognize the .backupdb because it can't back up to that anyways. You could try creating a .sparsebundle of your TM drive via disk utility, then naming that correctly and placing it on the networked drive, but I'm not sure if macOS will recognize it.