I'm going to make a big assumption and guess that your car is a B5.5 like mine. That being said,
To fish the end out of that prohibitively small space and not have to remove your door, run a length ( I just fed it right off the spool) of thick weedtrimmer line down from the roof drain inlet, you'll see it inside the grommet hole after it has come through the drain hose. You can then grab the trimmer line-might have to use something to hook it and then guide the bottom of the drain hose out of the grommet hole. There's not a lot of excess, and you don't want to pull on the drain hose as you might pull it free of the roof drain up top (ask me how I know this is possible

) In my particular case, I'd misplaced my grommet somehow, so I simply obtained a piece of clear vinyl tubing from Lowe's and used it as a sleeve to fit
over the drain hose, sliding it about 6 inches up the drain hose, adding enough length to extend well out of the pillar grommet hole. It's worked like a charm ever since. When I eventually find the grommet piece, I'll cut that dirt-catcher tip off of it, and reinstall it properly. Utilizing the trimmer line as a guide (anchored up top to keep it taut), you can feed the grommet back into place on the drain tube, making sure it's well seated. Then, put the grommet gently back into its hole. Of course, pour a couple of ounces of water down the drain up top, to verify that it's properly coming out the grommet end because, well... Murphy's Law.
long story short, yes, you need to either reconnect the line to the drain nipple, or otherwise route the flow out of the body of the A pillar.