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Default Auto Filter Sorting Issue

I have a large spread sheet and frequently use the auto filter capabilities.
My rows are getting out of sequence (the data is not staying in the correct
row). I've marked cells and then tested by sorting different columns
ascending, desending, etc. and I've done this on multiple columns. I can not
get the data to return to the original format even when I turn the filters
off. I have in excess of 100 hours invested in this data. Needless to say
it's a very important document! Any help will be greatly appreciated.
 
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