You can use rclone ls to test filter flags and see what the output is.
I'm still really not following on what you are trying to do and what the issue is.
If you exclude something in a filter, it won't modify the destination with said filter.
felix@gemini:~/test1$ rclone sync --exclude test4.out /home/felix/test1 /home/felix/test2 --dry-run
2021/01/05 08:21:18 NOTICE: test1.out: Skipped copy as --dry-run is set
2021/01/05 08:21:18 NOTICE: test2.out: Skipped copy as --dry-run is set
2021/01/05 08:21:18 NOTICE: test3.out: Skipped copy as --dry-run is set
felix@gemini:~/test1$ rclone sync --exclude test4.out /home/felix/test1 /home/felix/test2 -v
2021/01/05 08:21:25 INFO : test1.out: Copied (new)
2021/01/05 08:21:25 INFO : test2.out: Copied (new)
2021/01/05 08:21:25 INFO : test3.out: Copied (new)
2021/01/05 08:21:25 INFO :
Transferred: 300M / 300 MBytes, 100%, 1.327 GBytes/s, ETA 0s
Transferred: 3 / 3, 100%
Elapsed time: 0.2s
felix@gemini:~/test1$ ls ../test2
test1.out test2.out test3.out test4.out
felix@gemini:~/test1$ ls
test1.out test2.out test3.out test4.out
felix@gemini:~/test1$
Another example with a directory.
felix@gemini:~/test1$ rclone sync --exclude test4.out --exclude test4/** /home/felix/test1 /home/felix/test2 -vv
2021/01/05 08:23:31 DEBUG : rclone: Version "v1.53.3" starting with parameters ["rclone" "sync" "--exclude" "test4.out" "--exclude" "test4/**" "/home/felix/test1" "/home/felix/test2" "-vv"]
2021/01/05 08:23:31 DEBUG : Creating backend with remote "/home/felix/test1"
2021/01/05 08:23:31 DEBUG : Using config file from "/opt/rclone/rclone.conf"
2021/01/05 08:23:31 DEBUG : Creating backend with remote "/home/felix/test2"
2021/01/05 08:23:31 DEBUG : test4.out: Excluded
2021/01/05 08:23:31 DEBUG : test4: Excluded
2021/01/05 08:23:31 DEBUG : test4.out: Excluded
2021/01/05 08:23:31 DEBUG : test1.out: Size and modification time the same (differ by 0s, within tolerance 1ns)
2021/01/05 08:23:31 DEBUG : test1.out: Unchanged skipping
2021/01/05 08:23:31 DEBUG : test2.out: Size and modification time the same (differ by 0s, within tolerance 1ns)
2021/01/05 08:23:31 DEBUG : test2.out: Unchanged skipping
2021/01/05 08:23:31 DEBUG : Local file system at /home/felix/test2: Waiting for checks to finish
2021/01/05 08:23:31 DEBUG : test3.out: Size and modification time the same (differ by 0s, within tolerance 1ns)
2021/01/05 08:23:31 DEBUG : test3.out: Unchanged skipping
2021/01/05 08:23:31 DEBUG : Local file system at /home/felix/test2: Waiting for transfers to finish
2021/01/05 08:23:31 DEBUG : Waiting for deletions to finish
2021/01/05 08:23:31 INFO : There was nothing to transfer
2021/01/05 08:23:31 INFO :
Transferred: 0 / 0 Bytes, -, 0 Bytes/s, ETA -
Checks: 3 / 3, 100%
Elapsed time: 0.0s
2021/01/05 08:23:31 DEBUG : 2 go routines active
felix@gemini:~/test1$ ls ../test2
test1.out test2.out test3.out test4 test4.out