I was just switching a reel over to my St. Croix BASS-X casting rod and noticed the liner of about the 4th guide from the tip is missing.  I’m not sure I want to bother paying shipping/fees for a warranty repair to fix that.  Is one missing rod guide liner a big concern?  I guess I should run a cotton swab in there to see if there are any sharp edges or burrs?

Usually if you contact them they will send you everything and they will tell you how to fix it, avoid all the fus. Same thing happened to me. And now I am good as new. They sent the guide and glue and instruction and some tool I think.

I would definitely replace a guide with a missing insert. 

 

Look for a local rod builder if you don't want to mess with it. It should be pretty cheap to replace a guide.

Local builder should be able to replace the guide quickly, 2-3 days to strip, rewrap and then put 1-2 coats of finish on at most. Most bass rods are single foot and single color, super easy to replace. Hardest part will be matching the exact guide, if you can get that info or even have st Croix send you one it will go a lot easier for the builder to take care of it. 

Lots of fly tying shops are set up to replace them if you have one in your area.