Normally the root canal in the earlier days before the invention of rotary endodontics used to be 5 days Procedure. But nowadays its single visit single sitting RCT. You have mentioned that your dentist has cleaned the root canal and dressed it temporarily. Well that is like the old conventional procedure or another point may be your tooth has a chronic infection with pus . But, either way it's unharmful

Usually the Endodontist will keep the medicament inside the canal if the tooth is going for the second or third visit of r.c.t...and to prevent any extra infection to the root canal from oral fluids it has to be closed with temporary filling.... it's safe.