It sounds similar to buggy behavior I just reported near the end of last week. Here's what I've been seeing.
1. In Listing view mode for a deck, when I save a custom edition setting for a card, it goes back to displaying the default of whichever Pricing mode I've selected (i.e. either "Last Main Printing" or "Default").
2. When I go in to edit a custom edition, while in editing mode for that card, it shows whichever edition I had last saved as custom, but always reverts as per item 1 when I click save.
3. When I switch to Spoiler view mode, it will show whichever custom edition I had last saved (even though it isn't showing it in Listing view mode).
4. When I go into my inventory, I will see a count of "0" for any card edition I have assigned as a custom edition, instead of counting the number I have assigned of that edition as custom. It will also no longer be counting that card's default selection as in a deck.
This is what it currently looks like in practice under the following scenario with Apprentice Necromancer in a deck, a card I own two editions of (Urza's Destiny and Commander 2017).
1. In Listing view mode, I see it as belonging to Ultimate Masters when I select pricing mode of "Last Main Printing" and Commander 2017 when I select "My Inventory."
2. When I go in to edit my custom edition on that card, I see it set to Urza's Destiny until I click save and leave editing mode for that card in my deck.
3. When I switch to Spoiler viewing for that deck, I see the Urza's Destiny image for the card.
4. When I go to my inventory, I see 0 copies of my Urza's Destiny edition in a deck, and 1 copy of my Commander 2017 edition in a deck (because that second copy is in a different deck).
5. I also tried setting my Commander 2017 copy in its respective deck to a custom edition of Commander 2017, which is the same as its default value...and now I see 0 copies of that edition as listed in a deck in my inventory.
