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For the second application/issue, I would use a deduplicating backup program like restic or borgbackup, rather than trying to manually keep track of "patches" of diffs. The restic backup program allows you to back up directories from multiple machines to the same backup repository, deduplicating the backup data both amongst fragments of files from an individual machine as well as between machine. (I have no user experience with borgbackup, so I can't say anything about that program.)

For the second application/issue, I would use a deduplicating backup program like restic or borgbackup, rather than trying to manually keep track of "patches" or diffs. The restic backup program allows you to back up directories from multiple machines to the same backup repository, deduplicating the backup data both amongst fragments of files from an individual machine as well as between machine. (I have no user experience with borgbackup, so I can't say anything about that program.)

$ ls -lh
total 626208
-rw-r--r--  1 kk  wheel   153M Feb  3 16:55 abc
-rw-r--r--  1 kk  wheel   153M Feb  3 16:56 abc2

We create out patch and call it abc-diff:

$ ls -lh
total 626208
-rw-r--r--  1 kk  wheel   153M Feb  3 16:55 abc
-rw-r--r--  1 kk  wheel   153M Feb  3 17:02 abc2

We create out patch for transforming abc into abc2 and call it abc-diff:

For the second issue, I would use a deduplicating backup program like restic or borgbackup, rather than trying to manually keep track of "patches" of diffs.

For the first issue, calculating and storing a diff of the abc and abc2 files can be done with rsync.

Re-applying the patch a second time seems safe. There is no error messages nor does the file's contents change (the MD5 checksum does not change).

For the second application/issue, I would use a deduplicating backup program like restic or borgbackup, rather than trying to manually keep track of "patches" of diffs. The restic backup program allows you to back up directories from multiple machines to the same backup repository, deduplicating the backup data both amongst fragments of files from an individual machine as well as between machine. (I have no user experience with borgbackup, so I can't say anything about that program.)

Calculating and storing a diff of the abc and abc2 files can be done with rsync.

Re-applying the patch a second time seems safe. There is no error messages nor does the file's contents change (the MD5 checksum does not change).

Note that unless you create an explicit "reverse patch", there is no way to easily undo the application of the patch.