Do you mean that he actually has two lines inserted or that the PICC line has two ports (tubes) coming out of it?
I've had PICC lines placed several times (my veins are HORRIBLE, so most of the time whenever I have to go to the hospital they have to give me a PICC line because a regular IV never seems to work). Mine have always been one line that has two ports (tubes) coming out of the main line (the part that has been inserted into the body). I've also a couple of times had TPN feedings done through the PICC line while in the hospital.
In my case, they usually (but not always) used one of the ports for INgoing things such as IV and meds and the other port for OUTgoing things such as blood draws. Although, if they were having trouble with the OUTgoing port clogging or not running as fast as they thought it should, they would sometimes use the other port to get my blood draws. So therefore, I'm presuming that there is no danger or trouble if the ports get reversed or mixed up.
The only problem I can possibly think of is that, just as with oral antibiotics, some of them do not mix well with certain food and drink - and I'm thinking that may possibly be the case with the IV antibiotics. Perhaps they suggested keeping one port specificaally for the nutritition due to a possible problem with the mixing of the antibiotic and the "food".
Obviously, I'm no doctor or a nurse, simply giving my own experience with PICC lines. If your father has two distince PICC systems inserted, then I would definitely think they intended to keep one specifically for nutrition and the other for antibiotics and other meds.
I would suggest simply asking his nurse about this - mention to him/her that the nurse that placed the PICC line/s told you that one was to be for nutrition and the other for antibiotics and you're wondering if there is a difference in them and if it makes any difference if they are inadvertently mixed up.
I hope your father feels better real soon.