I would use a plastic putty knife to remove the old caulk and be careful not to damage the roof membrane. You can try heating it up with a hair dryer or heat gun.
Depending on how bad the seal is, you can just apply new caulking over the bad areas of the existing caulking.
Here is a link to Alpha systems, which is most likely the manufacturer of your roof. There is good information on the care and maintenance of the roof in the FAQ section.
https://www.alphallc.us/product/roofing/
They recommend using a household cleaner to clean the area before applying new sealant. I use 409 and spray it on my towel not directly on the roof. It seems to work pretty good.
Edit- I recently found a big crack in the sealant on my front cap. I cleaned the area and added some Dicor self leveling.