Will backing up files also include files that are marked for deletion?

Solution 1:

No. Time Machine only backs up files present on the filesystem and furthermore, only those not excluded by a rule or explicit exception.

• On OS X, what files are excluded by rule from a Time Machine backup?
• What does Time Machine back up?

Solution 2:

Time Machine does not backup deleted files. The whole point of maintaining a backup is to make copies before files are deleted -- so that if you want to restore them after deletion, you can do so.

It is not useful to think of deleted files as merely 'marked for deletion but still there'.

Having said that, the APFS format does make 'local snapshots', which are alternative catalog entries to older data, including deleted files. So if you're looking to recover deleted files that have not been previously backed up by Time Machine, then the local snapshots may preserve them.

You can browse local snapshots by entering the Time Machine app when the external backup drive is NOT connected. About local snapshots