The issue with the rubber boot is that it has to be seated correctly if it is removed. The rubber boot is shaped a little like a top hat with a brim. The brim contains a round spring, like a key ring. The bore in which the boot sits narrows just in front of the circlip, and it forms a step. The brim of the top hat is slightly larger than this narrow bit, so it has to be pushed over that step so that the key ring spring is squeezed and it grips the sides, forming the seal and keeping it in place. The step is angled slightly, so pushing it into place will help the circular spring to compress. But you can feel when it pops over that step to seat properly.
This does two things:
1. It forms a proper seal to keep water out of the bore of the SMC
2. It moves the brim of the top hat seal behind the water escape channel.
If that boot is removed and is not put back properly, the brim will block the water escape channel, and water will pool near the brim. The pooled water can then get behind the boot because the brim isn't sealing properly. It is not easy to seat the rubber boot properly - you need to be able to push the brim equally around its circumference in at least 3 different positions. And that risks puncturing the rubber. Really, it needs a tube, but you can't get a tube in without undoing the bracket, and that risks altering the critical length of the SMC push rod.
Best to leave it alone as Larry suggested.
Here is an article that I wrote about this with some illustrations.
The rubber boot on the ST1300 Secondary Master Cylinder is designed to keep water out. Unfortunately, since you cannot see what you are doing when fitting the rubber boot, it is entirely possible that casual maintenance can result in allowing water to be let in. I made reference to this in the...
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