I think you need to setup in Plex a “temp” directory in order to transcode
Go into the server settings and look for that particular setting, set it to use your external drive (choose a directory) the files it generates are temporary
https://support.plex.tv/articles/200250347-transcoder/
Find the files that are clogging up your SD card then delete them after you change the temp folder to a folder on your external drive (or even create one)