You exclude files and not directories. So if you want to exclude files in a directory you need to match the file and path. And yes you'd want to use sync.
**/*.sdr/**
Unless I'm reading what you're asking wrong. Warning I haven't finished my coffee. 
ref: Rclone Filtering
Edit: The first slash though will cause you issues if its in the base. You may want this.
--exclude="**.sdr/**"
dell-xps:~$ rclone ls dest/MATH416 --exclude="**/*.sdr/**"
2 416.pdf
2 Exam.pdf
2 416.sdr/metadata.pdf.lua
dell-xps:~$ rclone ls dest/MATH416 --exclude="**.sdr/**"
2 416.pdf
2 Exam.pdf
dell-xps:~$ rclone sync --dry-run MATH416 dest/MATH416 --exclude="**.sdr/**"
2021/07/08 08:40:05 NOTICE: 416.pdf: Skipped update modification time as --dry-run is set (size 2)
2021/07/08 08:40:05 NOTICE: Exam.pdf: Skipped update modification time as --dry-run is set (size 2)
2021/07/08 08:40:05 NOTICE:
Transferred: 0 / 0 Byte, -, 0 Byte/s, ETA -
Checks: 2 / 2, 100%
Elapsed time: 0.0s
dell-xps:~$ rclone sync MATH416 dest/MATH416 --exclude="**.sdr/**"
dell-xps:~$ find MATH416
MATH416
MATH416/Exam.pdf
MATH416/416.pdf
dell-xps:~$ find dest
dest
dest/MATH416
dest/MATH416/Exam.pdf
dest/MATH416/416.sdr
dest/MATH416/416.sdr/metadata.pdf.lua
dest/MATH416/416.pdf
dell-xps:~$ mv MATH416/Exam.pdf MATH416/Examination.pdf
dell-xps:~$ rclone sync MATH416 dest/MATH416 --exclude="**.sdr/**"
dell-xps:~$ find dest
dest
dest/MATH416
dest/MATH416/416.sdr
dest/MATH416/416.sdr/metadata.pdf.lua
dest/MATH416/416.pdf
dest/MATH416/Examination.pdf