if there are factors that force the book to be resynced (new version of ID) then its one at a time... but that will be the last time....G
It will only happen once (and frankly, what you are doing is a very bad idea).
When you open the old book in CS5, you are converting to the new format. All of the legacy files also need to be converted, even if added to a new book in CS5.5, hence the Save As since ID will not overwrite the old versions until you tell it to (and that's the bad idea). I strongly recommend (though it's too late for any books you've already updated and overwritten) that you either continue to edit in the old version, or that you take the time to open each file in the original version if it's older than CS5, then export to interchange format (.inx or .idml, depending on version), open those files in CS5.5, save with new names so you don't overwrite anything, then add to a new book and proceed.
One of the reasons I recommend this seemingly time-consuming approach is that there are too many reports (another one yesterday) of some sort of problem that pops up late in the editing cycle when converting legacy files to CS5/5.5 by opening them directly and saving. This is a belt and suspenders insurance approach, and is far less labor intensive than starting over, which might end up being your other option down the road if something goes wrong.