Hi @ShonB,
the export command is working as expected, returning one sequence file containing all the representative sequences which a re not mitochondria and not chloroplast (assuming the filtering step worked as expected). In this sequence data there is no information indicating which sample contain the sequences, so the best it could do is return them all in the same file.
If you want to get a sequence file for each sample you could work with some scripting as @timanix suggest or try to apply a filtering exporting step for each single sample you need to check, as described in:
Hope it helps
Luca