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Reiterating the comments as an answer for the convenience of others: Always make sure that each layer has a unique shapefile associated with it, otherwise data losses will be likely if more than one layer is based on the same shapefile and you edit its attributes.
Those are actually two different things. Geoprocessing tools don't honor the split policies of feature classes or tables as noted on most of help pages for the tools - this one for example (look for the yellow triangle exclamation point). Those are the policies set using domains, and where that third option of Default comes in. As far as I know, this ...
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