And if try to place a text box on any of these blank pages I get a message that says "Requested operation would cause one or more objects to be too small. Please check stroke weight.
Or if I try to place an image, I get a message that says: Unable to set bounding box.
It gets weirder. If I "Select all" on these new blank spreads, a tiny box with blue borders (it looks like stacked pages) appears directly in the middle of the spread. If I click on it, a blue rule line shoots out diagonally to who knows where (out of the workspace).
Diagonally shooting blue rules are the default for Threaded text frame indicators.
You're getting close.
At somepoint, after a selection, set it's placement to x = 0 y=0,
Sorry for all the posts, but I guess more info is better than less.
Another symptom is when I try to paste anything on the strange blank pages, the workspace area for those pages gets really wide. If I zoom out, it shows the width of these workspaces are ten times wider than the normal pages.
These blue rule lines go out of the workspace. When I zoom out all the way I can see them go out of frame.
The current X, Y is the text box size in the document, 6", 4.5". Changing this to 0, 0 just makes the workspace for these pages creazy wide.
I've seen this, or something similar, twice before here. ID has somehow munged the coordiantes and dimensions of the frames. You can try an export to .idml, but my recollection is it won't help.
You can also try making a copy, then delete the empty (and other bad) pages. Your text should stay threaded, but you'll lose loose images. No guarantee on that either, not any guarantee it won't recurr, so I'd export the stories to ID tagged text and rebuild. I think something else besides ID that you are running is probably responsible, but I have no idea what it might be.