Everyone,
I just finished up a week-long back and forth with Apple regarding this issue. What they had me do was this:
First they had me create a before and after folder with data to send to their engineers. You do not need to do this, but create a folder on your desktop called "Back-up" anyway.
Quit iTunes
Open Finder
Click on user data - this is probably your name
Select Music
Select iTunes
You will see two files in there, one called "iTunes Library.itl" and one called "iTunes Library.xml." Copy both of those files into your "Back-Up" folder on your desktop. This is just for a precausion.
Then,
Delete the iTunes Library.itl. You have a back-up in the back-up folder if you need it again.
Then,
Select Previous iTunes Libraries
This folder will have several files that are previous versions of your iTunes library. I'm not sure how often they update, but it might be with each upgrade of iTunes. Anyway, you need to find the most recent one. Mine was from 12-4-12.
Then,
Take your most recent Previous iTunes Library, which will read "iTunes Library (DATE).itl"
Move that file into the iTunes folder, where the previous iTunes Library.itl was.
Delete the date from the name of the file. So it now reads "iTunes Library.itl"
Close Finder
Open iTunes
This restored my play counts that were missing, and so far it has fixed the issue of them dissapearing. I have updated both my iPod and iPhone (which were seemingly triggering the error) and all my play counts remain.
There are a few issues, though. This will reset your library to how it looked on that previous date. So a couple albums I bought from iTunes between 12-4-12 and 12-22-12 were missing and needed to be re-downloaded. That was no problem, because you can re-download everything that you have purchased from the iTunes store.
Also gone were a few songs that I uploaded from CDs (the old fashioned way). I'll have to put those back on manually.
Also gone were any additional plays between 12-4-12 and 12-22-12.
If you have songs that you manually uploaded, or purchased from another site, I recommend backing those up before doing this. If you are super into your play counts (which most of us probably are since we freaked out about this in the first place), and you don't want to lose what has been played since your last "Previous iTunes Library" file was created, I recommend selecting all of your songs before doing the steps above, hitting "Command C" to copy them, and then pasting them into an Excel spreadsheet. It will keep all of your data in one spot, and you can manually edit the songs that need the additional plays if you want.
It would be a time consuming process, but at least it would be accurate.
I feel relieved now that this issue has been put to bed for me. I hope everyone can follow the steps above and fix the issue on your computers.