I believe Ancestry simply doesn't display both. When you are in pedigree view on Ancestry you may notice the active person is in brown. When the file contains ancestors for the spouse you will see little 'rabbit ears' for lack of a better term, on their tan icon. When you click on the spouse, the spouses box turns brown and the original person turns tan and gets the rabbit ears indicating they have a tree but it is not displayed. Both locations should have the identical number of people in the file.
Question for you. In going back and forth - has any data been lost? I know for example if you put anything in to the "Comment" field on ancestry it will not come down in a GEDCOM in to their own software Family Tree Maker. I am specifically interested in RootsMagic though - I only gave that as an example.