Is it normal when working on a mod that if you select an esp for a master file, that esp will not be shown to be a master when reloading what you were working on?

What?

ESM is a master file.
ESP is a plugin file.

The Geck only makes plugin files. If you want to edit an existing plugin file, you select it and click the 'set active plugin file'.

Maybe I didn't type this right.

Let's just say I want to make a new esp that uses assets from an existing esp. After I create the new esp, save it, then reload, the existing esp which I selected as a master is no longer in the list of masters of the new esp.

Question: why?

The Geck removes the esp from the master list because the esm flag wasn't set in it. So basically you lose everything you just did. There is no way to change this behavior. So leave the esm flag set in the esp that you want to master off of. Use FNVEdit to toggle the flag so that ONAM records (if any) are updated properly.
When you are all done with your new plugin, you can turn off the esm flag and it will still work as a master for your mod. The game exe doesn't care, but the Geck does. Just don't forget and load up you mod again with it unset!

That's what I've been doing. Just an annoying extra step that I was hoping to get rid of. Oh well...