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The master cylinder is directly underneath the fluid resevoir. The Resevoir mounts to the master cylinder. If you would like an image enter "2001 BMW 325 master cylinder" into a search engine, under the image option.
The master cylinder supplies the pressure to the brake fluid that travels between the maste brake cylinder resevoir and the brake caliper pistons (through the brake lines. If the master cylinder fails there will be insufficient compression of the brake fluid to make the calipers operate as designed. Leaks in the brake lines and/or cylinders is a possibility, and unrelated to functionality of the master cylinder. Also, pistons located in the brake calipers can form a corrosion ring on their inside walls if there is breakdown in the brake fluid or moisture that gets into the lines. Operating the vehicle when there is insufficient brake fluid in the master cylinder resevoir can also lead to air getting into the brake lines, causing bad working brakes. Air compresses more than brake fluid, and the master cylinder isn't designed to compress air in the brake lines. Sounds like a bad case of "lack of maintenance", as opposed to bad advice from the mechanics. That said, there's no excuse for bad installation. But, it's tough to improperly install a brake line since they are nothing more than hollow metal tubes. There should be no rubber connectors installed in the brake lines. When bleeding the brake lines one must remove all of the trapped air before you will see any fluid appear. If the valves in the master cylinder are not properly operating the master cylinder will not allow the brake fluid to get into the brake lines.
Open the bleeder screws on your brake, and stick a gas line hose on the bleeder screw. Put the other end in a clear bottle of brake fluid, and pump the brake till all the air bubbles quit coming out. Then tighten the bleeder. If no bubbles come, you may have a faulty master cylinder.