Noob question about factories. As I understand it factories produce additional production points which are used to build ships,pay for upkeep on ship already build and other things. My question is once a planet maxes out on the number of factories it can have will they still produce even if I lower the industry bar?

Yes.
The Industry bar is to buy factories or, if you have max amount of factories, to generate BCs for your Reserve.
You don't need to tell the factories to produce.

OK that's how I though it worked I just wanted to make sure . Think I might be putting some of my planets in to R&D overdrive.

No, not R&D, just reserve and putting this reserve will not really cause overdrive per se, but you can use it really good for disasters quick building and similar. There is a kind if loss involved but I do not remember the ratio.

But I do remember good for shields on poor/ultra poor, solar flare and so on ;)