Your question is so short so the only way to answer it is to speculate. If possible, please, clarify what you mean.
Without context I would say that changing of SESSION ID shouldn't affect "current login" or data binded to initial testing.
Another question is how you are altering session, because can't just take arbitrary number and use it as new ID. Probably, you use specific initialization procedure which returns you valid initialized session and session ID. New session is in the initial state, so its data isn't in the proper state for operation which can be performed with the data from old session, and simple replacement shouldn't work.
It backs up what I was saying about a sesison hijack meaning game over.
What is comforting from my point is that the attackers did pretty much exactly what I wrote in the order I wrote.
but they went further by uploading shells.