Hello,
I think, if I’m understanding what you’re trying to do, there’s not necessarily a reason to be using custom-filtered decks in quite the way that you are using them.
If you’re studying, say, pulm every day it might be easier to just build a subdeck, rather than building, and rebuilding, custom-filtered decks every day.
An easy example would be below. I took this from the MCAT deck as an easy example, though the idea would be the same:
If I wanted to study only Biology, I could just move the Biology cards to that subdeck and click on that subdeck to study. No need to rebuild custom-filtered decks each day; you just click on the deck and study whatever cards happen to be due.
If I’m understanding what you’re trying to do, I think this would be a lot easier, and lower-maintenance, while still allowing you to focus your primary efforts on your current block material.
A custom-filtered deck can be useful on occasion. Say, the day before an exam you want to review only the pulmonary vasculature. Or before a specific rotation you want to brush up on the peritoneum or whatever. But custom-filtered decks aren’t typically as well suited for everyday use in this way, as it also sounds like it’s causing you a fair amount of extra work and some frustration. 
Please let me know if the explanation I gave above makes sense, and if you have any other questions. I know Anki can be a bit bewildering at first but I’m confident we can get you where you want to be.