There is currently no reason to suspect that the update will break anything permanently, but it may require you to change the paths to the DB directory in DT.
I would guess it is fair to assume that any other software which relies on files being at the end of a path is likely to react adversely to that path changing without the software being told… however, I hardly think the DT forum is the right place to ask how EF is planning to handle the impending changes.
At the moment, my interpretation of the situation is: be aware, have backups, change paths when necessary.