Thank you so much for your help, John!

However, I was about to post a workaround I just found: since it is always master 1 that disappears and never master 2, I made a duplicate of master 1 - say master 3.

When selecting all the slides that follow master 1 and assigning them (via Home > Layout) to master 3, master 1 disappears but masters 2 and 3 stay. So now I can switch and keep switching between masters 2 and 3. Which is what I needed.

But I'll keep in mind your advice on the logo. Is it better to add the logo to the different layouts instead of the master? (as you can guess from this question I'm not at all familiar with XML editing)