So I've been working feverishly on a whole new worldspace, a new city with buildings, roads, highways, etc. I worked for about 4 hours on it just yesterday, and when I go to load up the GECK today, I open the .esp up and almost everything is deleted. Gone. It even has removed several cells.

Now I notice every time I open up my mod file it deletes even more, usually the stuff that I placed earlier. All that remains are the objects I placed at the end before saving and quiting; however, if loaded up a few more times it seems that the GECK with remove those as well.

What could possibly be the problem here? This is extremely frusterating as hours of work has gone to waste as the GECK seems to want to delete anything I create.

Any ideas here?

If you are certain you use the last version of the geck (V1.4) open your mod in FNVedit and look for duplicate groups !!!
As strange as it seems the geck can become crazy and create a duplicate group for objects, cells, anything, in fact, and place everything you add in the ghost group. Of course it doesn't work. If so, you can merge the groups and it will return to normal.
I hope for you it is the problem here, otherwise I have no idea.