They may or may not be FULLY charged but they won't be totally dead. Just put them in the charger before using them and when the light turns green they are done no matter how long they've been in there. Leaving them in the charger any longer after the light turns green will not do any harm but won't help any either.
Houdini is correct, I received some protected cr2's and put them on the carger and they hardly took any time at all to charge, so that means that they must have already contained some charge.
Also, do yourself a favor, get a multimeter so you can test the voltage on your
batteries. Some Battery chargers charge better then others, I have 2 identical chargers, when a battery that I had charged on one indicated it was done I checked it on the meter and it read that it was not charged to capacity, when I put the same battery back on the other charger the light was red and it continued to charge.