in first mission when I reach the village after destroying all the artillery installations, I meet a message that I have to destroy them all before entering. Could they recover while I was walking?
No, you should be able to enter the village after you destroy all of the Flak. Remember that to destroy them you must select the Attack icon while standing in their sector, after eliminating the artillery squad of course. Which version are you playing? Can you send a snapshot at zanklesoft (at) gmail (dot) com ?