converted file issue

Last night, I submitted a score into the PDF converter, which worked well enough for me to make some minor edits, but there is one major thing that I don't quite understand how to fix in musescore 3. The original score had a clarinet part, a cello part, and a piano part. I converted the cello part no problem since they're both C instruments, but it converted my clarinet part to a voice part, but it didn't transpose with it. so now my clarinet part is messed up because the transpose feature only moves the notes on the page where I need it without changing the sound. Is there a way to change the sound as I transpose the part? Both scores will be linked, and you will see my issue. Also, how can I remove those greyed out rests that it added in?