Digital BW, The Print

I have an original No More Carts, CIS, set up on an office printer 
(Epson 880) that my wife uses.  She didn't tell me that we needed 
more black ink until it ran out.  My concern is that because there is 
no more black ink in the bottle, and from the print output I'd guess 
most of the ink has been emptied out of the cartridge chamber, that a 
lot of air must have entered the lines.  If I just buy another bottle 
of ink now and switch it out, the CIS won't work, right?  I guess I 
need to use the vacuum pump again?  I have the original vacuum pump, 
but my concern with trying to suck out the extra air with the vacuum 
pump is that I'll also be sucking out whatever ink remains in the 
chamber/lines.  Do I need to buy a new CIS and start over or is there 
a way to fix this?  Thanks in advance for any suggestions.  Howard.