Yes, you're going to have to program this individually.
Here's my cheat:
Using the FX Generator, program ONE fixture for the fan/sweep in one direction to what you need. Save, generate, document(write it down on paper). Then, start over, repeat the process for the opposite fan/sweep. Hopeufully you end up withe same number of steps. Save, generate, document and now get to work.
You may need to repeat this as necessary to get the actual proper effect. I'm assuming you're only using 2 movers, but this could easily be replicated with many more.
Now, choose one of those FX scenes you generated and saved. You are saving often, right? using those notes and the correct fixture, modify each scene step as necessary(adding fixtures and values to fixture channels).
Dumbing it down for people who may be having trouble following:
Let's say I have two movers, one on each side of the stage. I want to start from them pointed at the center of the stage to moving OFF the stage(and then back IN). Let's look at this as two scenes: From center OUT and from OUT to center.
Let's assume to move the one on the left(audience left), it takes 6 steps using the FX generator to make a nice smooth move from center to outside. Let's say to do the same thing for the right mover, it also takes 6 steps to move from the center to the outside of the stage. Note that I created these moves from the FX Generator. I write down the values each one created.
Now, let's say I choose the LEFT SWEEP scene(center to left, using left mover) as my starting point, I then take my documented notes on the "center to right" scene, and then start adding them to the right mover on the "LEFT SWEEP" scene, which I've since copied and named "SWEEP OUT". Do your changes step by step and probably within a few minutes, it's all done.
Another option might be to do an X or Y inversion on one side's fixtures and match DMX channels. The downside is that you may not want a reversal all the time. This can be a good permanent and working option, but may not always provide the desired end results.
So, to confirm: Since NO TWO fixtures are doing the same thing, you'd have to adjust for each fixture individually, either on a scene by scene or step by step basis.