Here is a script I use to rename file extensions, but I don't know how you can run it from the ftp session. As I said in my previous post, you may have to schedule it through cron. Perhaps when you do your mget, the last thing you could do would be to do a put of a trigger file. Have a script look for that trigger file. When it finds it, run the code below to change the extension and delete the trigger file.
I got this code from someone on Tek-Tips:
Using pure ksh:
old_ext=pl
new_ext=pm
for file in $(ls *.$old_ext)
do
mv $file ${file%${old_ext}}${new_ext}
done