The simple answer is to allocate the cost based on relative values of the items acquired.
Naturally, there’s potentially a lot of room for interpretation there.
Some people like to look at various price databases, potentially including SMR, cardtarget, or others that are out there to attempt to assign those relative values. My experience is that almost every item has a potential range of values, and you could spent an entire career trying to get the math right. My approach is to spend a little time on it, get it close enough that it seems reasonable, and then move on.
Based on your example, it’s not uncommon for one (or two or three) item(s) to be a lot more valuable than the rest. Certainly it’s possible that $500 of your initial cost should be allocated to the item you sold, so you have no gain on that sale. Naturally, if you go selling 3 or 4 of them for $500 apiece, then you’re going to have a gain in there somewhere!
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