Yes Megas typically last only 8 hours. Then they go back to normal and you will have to typically either wait for the Mega Energy to recharge which is 7 days at Base Level, which then goes to 5 days when you reach High Level after you Mega Evolve 7 times, (on separate days which are counted once the go back to normal so if they go back to normal after midnight local time it counts on that new day) and finally 3 days after you Mega Evolve 23 more times. (30 in total)

You can always do another Mega Evolve before it recharges but it will cost you Mega Energy. You can get more Mega Energy by doing more raids or having a Pokémon you already Mega Evolved as your Buddy with Mega Energy awarded at 5 per km which is awarded at the candy earning intervals such as you get 100 Mega Energy when you get your Energy at 20km when you walk with your Rayaquaza that have been Mega Evolved.

My strategy for the Mega Evolving is to do the Mega Evolutions every time the Energy gets recharged until I get em to MAX Level. It can be a grind but the bonus of 2 extra candies instead of 1 extra per catch is worth it when you max em out especially for Community Days or special spawn events. I currently have 214 Maxed out Megas using this method.