I had recently taken over a local gym and put my Pokemon there to defend it, I collected my coins from the Defender bonus. This is the first time I've done that. There is a clock still counting down even though I have seen that my gym has been taken over already. Should I wait until the clock runs out to reclaim my gym or should I reclaim the same gym right away?
You can claim the gym right away, getting xp for it.
If you lose it, you can reclaim it (getting more xp, yay). If you don't lose it, you can get the coins as soon as the clock has counted down.
I think the best strategy is to drive around stopping at various gyms when you're defender bonus is ready to be collected. If you reclaim the gym then it will just get taken over again, so it's a bit of a waste of time.
Claiming them as you have your bonus ready means there is less chance of someone taking one over again, and even if they do you can just drive to another one and take it over so that you have ten. Then when you do just claim it right away and repeat the next day.
You can only collect the defender bonus once every 21 hours. If you intend to reclaim the gym for pokecoins, you will want to do it after the cooldown timer is up.
One of these answers are wrong. For every gym you have a pokemon in, you get 10 coins. If you have a timer still, you won't get coins. I have 5 hours left on my timer, so I'm going to wait until that time is up then go around to the gyms and try to beat them. Even if you are only in a gym for 60 seconds, you will still get the 10 coins. The important part is not to collect it right away, go around to gyms to see if there are any you can take over. It's better to put 5 pokemon in a gym and get 50 coins, rather than get a gym and collect immediately only getting 10 coins for the next 20 hours.
If you plan on battling an opposing team, and you are only really doing it for the coins, then put a weaker pokemon in the gym so you have your strong ones to go take more gyms. Like I said, if you have no timer, then if you put a pokemon in a gym for 60 seconds before it gets defeated, you will still get the bonus.
I'm not sure why that person said 10 coins is the limit, because it certainly is not. Last night I went and took two gyms, got 20 coins for them. Your pokemon do not need to [STILL] be in the gym to collect the bonus. I tested this theory, to see if my defender bonus would go back down to 10 if somebody takes one of the gyms I was in. They actually ended up taking over both if them, but I still had the 20 coins in my bonus. Just don't collect your Defender Bonus right away if you plan on trying for more gyms. I wish I had known this sooner.