This will also happen if you are exporting.
My suggestion is just make sure you have everything you want in one set and close the other folders.
Hope this helps!
If you have 2 personal folder files, they are independent of each other. Updating one is not designed to update the other, that is why it is not happening. As one microsoft rep said in a conference I attended “This is not a problem, this is a feature.” As Schmidtw suggests, just make sure ONE of the personal folders is accurate and then close the other one so it does not confuse you. You can close it by right-clicking on it and choosing close personal folder.