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Something is odd.
I have no problem such as you describe using the following proceedure:
Either select the pages you want to move in the pages panel of the "source" document and fromthe panel flyoout menu choose "move pages," or simply enter a range of pages to move in the dialog after selecting the command from the flyout menu.
Choose the new "destination" document and chosse if you will add the pages before or after the exisiting page.
In the destination the pages appear, and frames are threaded if they were threaded in the source, but no text is included in the thread before or after the section that was moved. You would still have any pages that were already in the destination document, but you should be able to delete them. If you have some keep option set to start on next odd page for the first paragraph of moved text, I think ID would add one extra page if the destination starts on page 1 and you move the pages after it, but again, you should be able to remove those extra pages.
thank'you to both