[Starson17]

Originally Posted by Marcy

If it helps at all, every time I tell calibre to "open containing folder" a new empty folder appears with a new number.

It's not being created when you "open containing folder," it's opening the folder that Calibre thinks holds your book.

For example I have a folder

Calibre Library > Chris Nicholson > The Elephant Keeper (1299)

This folder was created by Calibre previously.

but if I select The Elephant Keeper and choose "open location" a new folder is created:

Calibre Library > Chris Nicholson > The Elephant Keeper (1892)

This is where Calibre thinks the book is located. It's almost certainly not created when you choose "open location" as that code doesn't create folders.

Is there a way I can link my books back properly?

So, I guess what I'm asking is, is there a way for me to edit the metadata.db file to give all the books their proper numbers. I'd rather do that for 1700+ books that have to reimport them and re-edit all their metadata by hand.

I'd suggest this.
First, confirm what I wrote above (that the empty 1892 folder already exists.) I'm 95% certain, but doublecheck.
Next, check to see if you have the 1299 entry in your GUI main screen. I'm pretty sure from your post that you don't, but just make sure by doing a search or manually looking through to make sure you do not have these records at the bottom of your listing.
Third, I'm assuming that you have good metadata in the empty 1892 record, but no formats in that record. Also, assuming you do not still have the old entries (checked in step 2), open the 1299 folder (with a file explorer outside Calibre) and drag the book format files in it into Calibre's GUI.
This will create a third book id (lets say 1300), but without metadata.
Last, select both of 1299 (good metadata, no book formats) and 1300 (book formats, but no metadata) and choose the Edit Metadata, Merge-delete others to merge the two and keep your good metadata. (Preferably, select 1299 first, but it doesn't matter a lot.)

If you want, you can simply add the entire contents of your old library in one shot, then merge up all the records, or try to set Calibre to do this automatically for you (see below).

There are lots of different ways to do this that may make it easier. It may be best to move your library first using Calibre's new move library function. That will move what Calibre thinks are the correct folders and separate them from all the old folders (that Calibre seems to have forgotten about). Then, if you set set the regex in Add/Save correctly, and turn on the "If similar author title found ..." option, Calibre will be able to automatically match each new book to the correct old record (with good metadata) and you'll avoid having to do all the manual merges. Adding the old books should be trivial if you get them separated. It will take some testing to get it right, so if I was in your shoes, I'd back it all up and try several approaches to fix it, until I found one that would work well.
Good luck!