You said you've switched to files from and the error message says you should try using exclude.
I get:
felix@gemini:~/test$ rclone move /home/felix/test /home/felix/test/blah -vv
2022/11/29 16:20:09 DEBUG : Setting --config "/opt/rclone/rclone.conf" from environment variable RCLONE_CONFIG="/opt/rclone/rclone.conf"
2022/11/29 16:20:09 DEBUG : rclone: Version "v1.60.1" starting with parameters ["rclone" "move" "/home/felix/test" "/home/felix/test/blah" "-vv"]
2022/11/29 16:20:09 DEBUG : Creating backend with remote "/home/felix/test"
2022/11/29 16:20:09 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2022/11/29 16:20:09 DEBUG : Creating backend with remote "/home/felix/test/blah"
2022/11/29 16:20:09 DEBUG : Local file system at /home/felix/test/blah: Using server-side directory move
2022/11/29 16:20:09 INFO : Local file system at /home/felix/test/blah: Server side directory move failed - fallback to file moves: can't copy directory - destination already exists
2022/11/29 16:20:09 ERROR : Fatal error received - not attempting retries
2022/11/29 16:20:09 INFO :
Transferred: 0 B / 0 B, -, 0 B/s, ETA -
Errors: 1 (fatal error encountered)
Elapsed time: 0.0s
2022/11/29 16:20:09 DEBUG : 2 go routines active
2022/11/29 16:20:09 Failed to move: can't sync or move files on overlapping remotes (try excluding the destination with a filter rule)
and I add in an exclude
felix@gemini:~/test$ rclone move /home/felix/test /home/felix/test/blah -vv --exclude blah/**
2022/11/29 16:26:30 DEBUG : Setting --config "/opt/rclone/rclone.conf" from environment variable RCLONE_CONFIG="/opt/rclone/rclone.conf"
2022/11/29 16:26:30 DEBUG : rclone: Version "v1.60.1" starting with parameters ["rclone" "move" "/home/felix/test" "/home/felix/test/blah" "-vv" "--exclude" "blah/**"]
2022/11/29 16:26:30 DEBUG : Creating backend with remote "/home/felix/test"
2022/11/29 16:26:30 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2022/11/29 16:26:30 DEBUG : Creating backend with remote "/home/felix/test/blah"
2022/11/29 16:26:30 DEBUG : blah: Excluded
2022/11/29 16:26:30 DEBUG : Local file system at /home/felix/test/blah: Waiting for checks to finish
2022/11/29 16:26:30 DEBUG : Local file system at /home/felix/test/blah: Waiting for transfers to finish
2022/11/29 16:26:30 INFO : test: Moved (server-side)
2022/11/29 16:26:30 INFO : There was nothing to transfer
2022/11/29 16:26:30 INFO :
Transferred: 0 B / 0 B, -, 0 B/s, ETA -
Checks: 1 / 1, 100%
Renamed: 1
Elapsed time: 0.0s
2022/11/29 16:26:30 DEBUG : 4 go routines active
and
files from works for me without an exclude
felix@gemini:~/test/blah$ rclone move /home/felix/test /home/felix/test/blah --files-from /home/felix/filesfrom -vv
2022/11/29 16:28:57 DEBUG : Setting --config "/opt/rclone/rclone.conf" from environment variable RCLONE_CONFIG="/opt/rclone/rclone.conf"
2022/11/29 16:28:57 DEBUG : rclone: Version "v1.60.1" starting with parameters ["rclone" "move" "/home/felix/test" "/home/felix/test/blah" "--files-from" "/home/felix/filesfrom" "-vv"]
2022/11/29 16:28:57 DEBUG : Creating backend with remote "/home/felix/test"
2022/11/29 16:28:57 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2022/11/29 16:28:57 DEBUG : Creating backend with remote "/home/felix/test/blah"
2022/11/29 16:28:57 DEBUG : blah: Excluded
2022/11/29 16:28:57 DEBUG : Local file system at /home/felix/test/blah: Waiting for checks to finish
2022/11/29 16:28:57 DEBUG : Local file system at /home/felix/test/blah: Waiting for transfers to finish
2022/11/29 16:28:57 INFO : test: Moved (server-side)
2022/11/29 16:28:57 INFO : There was nothing to transfer
2022/11/29 16:28:57 INFO :
Transferred: 0 B / 0 B, -, 0 B/s, ETA -
Checks: 1 / 1, 100%
Renamed: 1
Elapsed time: 0.0s
2022/11/29 16:28:57 DEBUG : 2 go routines active
but if you have if buried somewhere and just have a file name
felix@gemini:~/test$ rclone move /home/felix/test /home/felix/test/blah --files-from /home/felix/filesfrom -vv
2022/11/29 16:29:52 DEBUG : Setting --config "/opt/rclone/rclone.conf" from environment variable RCLONE_CONFIG="/opt/rclone/rclone.conf"
2022/11/29 16:29:52 DEBUG : rclone: Version "v1.60.1" starting with parameters ["rclone" "move" "/home/felix/test" "/home/felix/test/blah" "--files-from" "/home/felix/filesfrom" "-vv"]
2022/11/29 16:29:52 DEBUG : Creating backend with remote "/home/felix/test"
2022/11/29 16:29:52 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2022/11/29 16:29:52 DEBUG : Creating backend with remote "/home/felix/test/blah"
2022/11/29 16:29:52 DEBUG : onedeep: Excluded
2022/11/29 16:29:52 DEBUG : blah: Excluded
2022/11/29 16:29:52 DEBUG : Local file system at /home/felix/test/blah: Waiting for checks to finish
2022/11/29 16:29:52 DEBUG : Local file system at /home/felix/test/blah: Waiting for transfers to finish
2022/11/29 16:29:52 INFO : There was nothing to transfer
2022/11/29 16:29:52 INFO :
Transferred: 0 B / 0 B, -, 0 B/s, ETA -
Elapsed time: 0.0s
2022/11/29 16:29:52 DEBUG : 3 go routines active
and with a files from:
felix@gemini:~/test$ ls -alR
.:
total 16
drwxrwxr-x 4 felix felix 4096 Nov 29 16:29 .
drwxr-x--- 9 felix felix 4096 Nov 29 16:32 ..
drwxrwxr-x 2 felix felix 4096 Nov 29 16:33 blah
drwxrwxr-x 2 felix felix 4096 Nov 29 16:33 onedeep
./blah:
total 8
drwxrwxr-x 2 felix felix 4096 Nov 29 16:33 .
drwxrwxr-x 4 felix felix 4096 Nov 29 16:29 ..
./onedeep:
total 8
drwxrwxr-x 2 felix felix 4096 Nov 29 16:33 .
drwxrwxr-x 4 felix felix 4096 Nov 29 16:29 ..
-rw-rw-r-- 1 felix felix 0 Nov 29 16:19 test
felix@gemini:~/test$ rclone move /home/felix/test /home/felix/test/blah --files-from /home/felix/filesfrom -vv
2022/11/29 16:33:28 DEBUG : Setting --config "/opt/rclone/rclone.conf" from environment variable RCLONE_CONFIG="/opt/rclone/rclone.conf"
2022/11/29 16:33:28 DEBUG : rclone: Version "v1.60.1" starting with parameters ["rclone" "move" "/home/felix/test" "/home/felix/test/blah" "--files-from" "/home/felix/filesfrom" "-vv"]
2022/11/29 16:33:28 DEBUG : Creating backend with remote "/home/felix/test"
2022/11/29 16:33:28 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2022/11/29 16:33:28 DEBUG : Creating backend with remote "/home/felix/test/blah"
2022/11/29 16:33:28 DEBUG : blah: Excluded
2022/11/29 16:33:28 INFO : onedeep/test: Moved (server-side)
2022/11/29 16:33:28 DEBUG : Local file system at /home/felix/test/blah: Waiting for checks to finish
2022/11/29 16:33:28 DEBUG : Local file system at /home/felix/test/blah: Waiting for transfers to finish
2022/11/29 16:33:28 INFO : There was nothing to transfer
2022/11/29 16:33:28 INFO :
Transferred: 0 B / 0 B, -, 0 B/s, ETA -
Checks: 1 / 1, 100%
Renamed: 1
Elapsed time: 0.0s
2022/11/29 16:33:28 DEBUG : 3 go routines active
felix@gemini:~/test$ cat ../filesfrom
onedeep/test
The more information you can share, the easier is for me to replicate/test/assist as I have more information to go on and I don't have to guess things.