You should remove the glass. This will benefit you two ways. 1. After removing the glass, clean the channel completely this will let you know what problems may lie under the sealer---hopefully none! 2. Not having to fit your new vinyl top to close tolerance around the old sealer is an advantage---it will give you more room to "trim to fit". Removing the existing glass is tedious but a section of thin strong wire wrapped around a wooden dowel on each end will easily cut through the old sealer and allow the glass to be removed. Clean up everything---install the new vinyl--reinstall the glass. Good luck.