It is not necessarily bad to do it more than once in a 12 week cycle. It is bad to do one movement for more than 3-4 weeks strait. Through much experimentation it had been determined that lifter can not continue to make progress on any one max effort movement for an extended period of time. Some people need to change every week others can go 3-4 weeks before they need to switch. This changes with your training age.
The essence of the conjugate training template is to let you continue to make progress well after this period is over. This is accomplished by rotating different movements that train different parts of the competition lift. For example board press trains the top part of your bench. Floor press takes away the leg drive and a large part of the lat involvement. Deficits dead trains the low end part of the deadlift. Rack-pulls train lock-out.
Test yourself to see where you fall. Try the same lift until you stop making progress. If you fail in week three then you know that you need to rotate every two weeks.
Personally, my upper and lower body are different. I can make progress on my lower body with same movement for up to 4 weeks, but I need change my upper body movement every 1-2 weeks.
Eventually, you learn to know you body better and you will know when it is time to switch.
Just some food for thought:
I train for raw strength, so I think it important to work bench with a full range of motion more often than geared lifters. I might rotated every two weeks between a full range movement and partial range movement. I might do something like this for an 8 week cycle.
Flat Bench 2 weeks
Board Press 2 weeks
Incline 2 weeks
Floor Press 2 weeks.
I pretty specific about why I chose certain movements.
Flat Bench - Because this ultimately what I am trying to make stronger.
Board Press - I do these with a pause and let the bar sink into the board. These really helped me learn how to stay tight and get leg drive.
Incline - I don't do a lot of shoulder work, I might rotate this with some overheads.
Floor Press - This is my weakest press and it really blasts the hell out of my triceps, which is my weakness in bench.
You could also rotate in close grip presses, but I like to keep these for supplemental stuff.
I don't currently use bands or chains in my max effort work, but they are also options.