Do you mean the vinyl stripping the glass itself actually sits in? If that's the case...
To remove the glass from the window frame, you will have to pull the whole thing out, unscrew the window frame from it's self, then remove the screws that hold the metal extrusions to the glass. Slip the weatherstripping off of the glass, wash/soak the weather stripping in hot soapy water. You may need a bristle brush to remove the dirt (I used a fingernail brush I bought at Wal-Mart of around $1). I simply washed all our weather stripping on the bus windows we reused. I still have a bag of most of the extras. I have the glass too. I don't know what to do with all that tempered glass. You may need to soak overnight. I also used a little bleach in my water (with laundry soap... don't use bleach with dish detergent) but we had bad mildew and moss on our weatherstripping. You may need to wet the weather stripping in hot water so that it will stretch better to get it back on the CLEAN glass. Use a razor blade to scrape the residue left from years of dirt and water. You will not get it all off. I think the dirt etches the glass over time and vibration. Put everything back together, Remove the old caulking/mastic. Clean bus side very well, especially if they used silicone. If silicone was used, you have to get it ALL off, down to clean paint. Use either mastic (comes in a tube like caulking) or a really good caulk (like a clear elastometric from roofing section or a 25 year or better door & window caulk - siliconized but not pure silicone). We used a 35 year siliconized latex caulking that we have used a great deal in the past. It took several days for it to dry out here in NM because it would skin over too fast which meant the interior cured much more slowly than we were used to. We learned to allow a week before messing with anyting we caulked in. I think the clear elastometic cures much faster (we have been using
Henry's 212 in many places) but is not water clean up.