By upgrades this far out you probably are just rebooking into a higher cabin and fare class, e.g. you are in "L" now and they quote you the price to go into "Z". The return trip doesn't have "Z" available but only "I" so it is more expensive.
Most accurate way you can find is to look up fares via expertflyer and you'll probably find that the $1000 = Z one way fare - one way for your already paid ticket -> the $1000 won't likely drop further.
If the $1000 upgrade is from your economy into e.g., "I" then it may be that if "Z" becomes available it does drop.

They also change fares within one letter class over time but not by a huge order of magnitude.