No, it should be able to work on nested sequences. A nested sequence is still seeing your origional edits, just in one track. If you double click on the nested sequence, you’ll see the origional clips in the origional sequence (usually ending with a .1). That is to say, your origional sequence is still there, its not like it turned into one file (i.e. an imported quicktime). That original sequence will still be 4×3. Another thing to think about….if this media was shot and captured at 4×3, when you make it anamorphic, you will be stretching the clips, making them distorted.