I want to reiterate a currently functional method for storing location info:
1. Create a virtual deck for each location and put them all in one folder.
2. When adding or removing physical cards, do the same for their virtual 'location decks'
To make finding locations faster, use a naming convention that makes them visually distinctive. For example, I precede each deck name with three hyphens. ( --- Trade Binder #1 ) That way, I can quickly find where the cards are even if the card page has numerous other decks mixed alongside the 'location decks'.
This same method works for regular decks as well. (I use "!" as a naming convention for those) Also, if you have a large main storage location like me, don't bother creating a deck for it; anything that doesn't have an affiliated 'location deck' can be inferred to be there. Even if it it's split among multiple boxes, as long as there are rules for those splits, (by rarity, set, color, type, foils, etc) it's easy to go straight to the correct box.
If a location's cards are added to the inventory without a 'location deck', just sort the inventory by date added and narrow down the first and last cards added from that location by checking inventory cards against the physical location. Then, just export that list and add it to the 'location deck'.
Example
Finding where specific versions of cards are can actually be relatively simple. Even in the not-so-simple Fireblast page below, I can determine where each copy is, due to a few organizational rules. I'll explain the process in detail.
Only 10 of the 15 have "---" or "!", so the other 5 must be in my big storage box, (categorized in the 6cmc red instants section) and consequently marked for trade. There are 8 total for trade, so the other 3 can only be in the "---" marked locations (My decked cards are rarely marked for trade). One of those locations is "--- Sealed DD: Jace v [Chandra]---", so clearly 2 of the 3 are there, and they're the 2 JVC versions. The last one for trade should be in the "--- Trade Binder #1", since that only contains tradelisted cards; of the tradelisted versions, the FNM foil seems the most tradeable (i.e. valuable). By process of elimination, the 4 gold-bordered editions and one Visions edition should be in the big box together.
That leaves 7 non-tradelisted Fireblasts: 5 are in regular decks (Goblins and Burn) and 2 are in the only remaining locations: Cube and EDH Foils. I prefer original-printing foils for cube, so that leaves the Fire and Lightning edition foil for the EDH Foils location, and the 5 Visions editions are in Goblins and Burn.
Deck names can store extra info. If, for some reason, I preferred the F&L edition in cube, I could record that exception in the notes of the Cube 'location deck' and make the name something like "! Cube (non-proxied) *E:Fireblast" with E for Exceptions, or just "! Cube (non-proxied) [Exceptions in notes]" so mousing over the title on the card page would alert me to click through and realize that the cube has a different edition than I would normally prefer.