Since Steam usually allows this kind of using a manual backup without problems with all games (you can have a fresh installation of Steam and actually move a complete backup of all your games there, only a couple of hundred Megs will have to be downloaded again), I guess something is wrong on the DayZ side in that respect. But even if it should actually be a Steam issue:
Why not get rid of the need for that workaround altogether and let people have two installations of DayZ all the time, one with an Experimental, the other with the Stable version? There will be two versions of DaySA for a long long time anyway... and making it easier for people to try out the experimental stuff on the fly should be welcomed by the Devs I guess.
Btw, the reason I found out was that I wanted to return to stable immediately after seeing that ungodly awful new server browser window :p