Alliance chests will be available depending on Kremlin status, so If you repair it you can take chests again.
Price for building repair will be decreased by 90%.
Also, important additional Info :
In the announcement of alliance change update there was a line "War is over when Kremlin is destroyed",
which actually means "War is over in the moment of restart if the Kremlin was destroyed at any point before the restart". Sorry for the inconvinience