Saving files over vs packaging.

I am curious about what the best file structure would be for files you use over year after year.
Being a publishing company and we produce updated editions each year. Each new year contains changes, corrections, new images etc.
For the past 3 years we have done a "save as" to each individual ID file and saved each file over to a new folder each year. This takes forever moving 65+ individual ID files! From my understanding is we don't move/copy paste files to the new folder since we've had problems with file corruption in the past and don't consider it the safest way. Is there any truth to that? Or any problems moving that many files? (We're on PC's only)
All these files and their images are stored on one drive so we don't have many issues with links breaking. But we've been doing a slow save as to each file for many years.
For instance 2010 Section One becomes 2011 Section One.
Each year we archive the older year's files by packaging them and moving the packaged files to a CD for backup. Then we do a save as to our 2010 files and save those files to 2011 renaming the files accordingly.
I suppose my point is what is the quickest most effective way to save files over each year? Would moving the packaged files be better? I know that would take far less time than what we've been doing, I'm just not sure at this point. Our system has worked great with no problems...it just takes forever and I don't think it's the most effective way to do this process each year. I hope I made sense here!
Thanks for any feedback!

You take about 2010 Section One to 2011 Section One?
So I presume there are more than one section? Have you not used the Book feature in Indesign, under File>New Book and then all the sections of a book go into a book file, which controls things like the pagination (if you want) and other things? You can then package the entire book (all the sections) at the same time).
You could also copy the sections to a new folder. Then use Adobe Bridge to Batch Rename all the files in the folder? Would that help? http://www.communitymx.com/content/article.cfm?cid=A4B43
From InDesign when you use File>Open there are 3 options  in the bottom left hand corner - you can choose to open the Original or a Copy and the Copy will open up as Untitled, meaning you can resave it anywhere. This works well if you're doing it on a file-by-file basis, and you can then save your files to the new location without worrying about overwriting the old ones.

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