Emptying rear brake reservoir but no leak

Actually, for practical purposes they are sealed by a rubber diaphram which sits between the fluid and the cover. As the brake pads wear the fluid in the master cylinder reservoir is used, displacing the outward movement of the caliper pistons as they compensate for the pad wear. The diaphram deforms preventing air from entering the reservoir. Air can get in between the diaphram and the master cylinder cap but not under it unless it's torn or installed improperly.

Since brake fluid is hygroscopic, it actively absorbs moisture. I try to purchase only what I need to bleed the system. Any extra is thrown out if I'm going to store it for any length of time. Apparently this stuff can absorb moisture through the smallest openings.
Actually, that's wrong. The diaphragm allows pressure to relieve when the brake fluid gets hot and expands. Then allows air in to compensate, trying to minimize water infiltration and brake fluid spillage. If you take it apart and inspect things you will find a small groove in the machined surfaces. The diaphragm itself is perforated to allow pressure in and out. Otherwise something would blow out or collapse under vacuum.
 
Actually, that's wrong. The diaphragm allows pressure to relieve when the brake fluid gets hot and expands. Then allows air in to compensate, trying to minimize water infiltration and brake fluid spillage. If you take it apart and inspect things you will find a small groove in the machined surfaces. The diaphragm itself is perforated to allow pressure in and out. Otherwise something would blow out or collapse under vacuum.
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I've taken many master cylinders apart over the years and the diaphram was never perforated. It is designed to move up and down with the brake fluid preventing air and moisture from entering the fluid reservoir. Now as the fluid level goes down a vacuum is created below the diaphram. Atmospheric pressure above forces the diaphram down with the fluid. It can also go up with expansion because the master cylinder cover is vented to atmosphere. So the only air entering is what is above the diaphram. You don't want air getting into the brake fluid reservoir mixing with the fluid.

This automotive master cylinder reservoir cover shows how the diaphram moves/distorts to displace the lowered fluid level. The diaphram rubber would need to be reset to it's flattened position after filling the reservoir. There are no holes in the diaphram...

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They are not sealed systems. Air is allowed in and out as the brake fluid moves to the calipers and back or there would be vacuum lock. That's why you get moisture contamination in your master cylinders. The front and rear master cylinders are separate and never comingle. There is no linked braking.
Interesting take on how the brakes work, however it's not entirely correct. The system is sealed from air (as much as posible) and the reservoir diaphrams allow the displacement of the fluid. The diaphragms expand and contract as fluid is displaced or returned in the system and air in the system is on top of the diaphragm, not the fluid. The ABS block ties the front and rear brake line systems together and is controlled by the ABS ECU. Ergo a combined brake system. The moisture that gets in the fluid is not because the system isn't sealed, it's because some leakage occurs around the reservoir diaphragms and caliper piston O-rings. In an ideal system there would no leakage and the fluid would never absorb any water. You are correct that the fluids don't comingle in so far as they don't transfer from one reservoir to another (my point about magic on disappearing fluid levels).

The second diagram below is the exploded view of the ABS system on the Rocket 3 (Gen 2). According to the manual the ABS system's ECU will actuate the rear brake with front brake lever pressure. Please read page 102 of your owner's manual, it should read thusly:
All motorcycle models are equipped with a partially integrated braking system, combined with the Anti-lock Braking System (ABS). This increases the braking efficiency when riding the motorcycle. When the front brake is applied, a small amount of rear brake is also applied, allowing for balanced braking. The amount of rear brake application is related to the level of braking force applied by the rider through the front brake lever. Use of the rear brake pedal alone will only apply the rear brake. For full brake effectiveness, always operate the front brake lever and rear brake pedal together.
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for what it s worth
brake fluid does not evaporate and personally i have never seen it boil (does not mean that it doesn't happen)
if you cannot find a leak it very well could be that it was never bleed right and was low at the beginning.
most of the time you will have air in the brake cylinder and when it gets hot it expands and forces the fluid out of the brake cyl causing problems.
very interesting debate on the closed system. i have never gave it much thought until now.
 
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