GISAID download augur input


im getting the hang of using augur + auspice, and this is more of a GISAID user gripe, but is there a way to download more than 5000 entries from GISAID at a time?

if I just used the GISAID download augur input option on multiple instances, does augur accept multiple fastas and metadata files? or do i have to merge them manually as single inputs first?