The two are not compatible. You can not wear foot orthotics if you want to wear flip flops. Generally you need a closed in shoe if you have to wear foot orthotics. This can prove to be a bit of a problem if you like wearing open shoe, especially if you live in a warmer climate.
Generally there can be nothing wrong in wearing flip flops from time to time and the change may be good for your feet. Just how much you could or should wear them is going to come down to the nature of your problem. You need to wear your foot orthotics as much as is needed to deal with the problem that the foot orthotics were made for.
Another option is to use flip flops that have arch support built into them or the recovery type flip flops that are made for athletes as they too tend to have some support built into them. A popular brand from Australia are the Archies which was designed by a physical therapist with some arch support in them.
This seem to be popular in Australia as an adjunct to foot orthotics; something to use alongside the foot orthotics in the right shoes. It obviously fits in with the lifestyles in Australia. They can be purchased here.