Do you want the green background on all pages? If so, putting it on the master page (and not releasing it on the document pages) will prevent your problem from happening.

Although the green block is, for practical purposes, on both pages, to InDesign, it's really only assigned to the left page of the spread. For example, if you start with this:

…which has a green box in the background, spanning both pages of each spread, and yellow boxes on odd pages and magenta boxes on odds…

…and you delete page one, you get this:

…where the yellow and magenta boxes have switched sides, but notice that the green box that had been across both pages is now only on the odd pages. That's because the green boxes were actually assigned to the even pages, which have now shifted to become the odd pages, and the box stayed with it's page.

Now, here's what happens when you delete page 2:

Except for page one, which hasn't moved or changed, the screen shots from removing page one and page two look the same, because I only removed one page at a time. That caused the pages to switch sides.

Now, here's what happens when you remove pages one and two at the same time:

This is what you are getting. As best as I can guess, the reason that the green box is above the yellow boxes is because the left page of the spread is higher in stacking order than the page on the right. My guess is that the stacking order of the objects on each page is reaffirmed when pages are deleted. And in this case, I don't think it matters whether you delete them one at a time or two. Here is a screen shot of what it looks like when I delete page one, then delete page two right afterward (actually, since page two had become page one, I had to delete page one the second time to delete the original page two, but you know what I mean):

This screenshot looks the same as the previous, even though this one had two pages deleted one at a time, and the previous one had two pages deleted together. I can't say whether this is a bug or not, but I assume that the engineers at Adobe didn't choose this behavior on purpose. It's probably a side-effect of some other choice that probably makes perfect sense.

I think the answer is to either  place objects that span a spread on the master, or to use layers if the master option isn't practical for the job you are doing.

I think the answer is to either  place objects that span a spread on document pages on the master, or to use layers if the master option isn't practical for the job you are doing.

@Michael – this is certainly true. But if we get a document from a customer or a colleague to work on, we could run into problems with that bug.

Uwe