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I just did a quick check of this in v3.46 and didn't have a problem (Windows 10, Surface Go with external HD monitor in "extended" mode). I don't normally use the Preview window undocked so I don't have long experience with this mode.
One trick I've used to restore window locations with other programs is to turn of, or otherwise blind the computer to the existence of, the second monitor temporarily. This forces Windows to move all windows to the main monitor.
What OS (exact version) are you using and what version of calibre?
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