It sounds to me like you have two conveyors that run continuously (as opposed to reciprocally). If this is the case you really don't need to perform specific homing function. I am assuming there is some speed relationship that, in a theoretically perfect world, once the flites are 'aligned' they would stay aligned.
Leadfoot is largely correct. Concentrate on getting the baseline speed relationships correct. After that you will need some type of sensor on each conveyor to tell you the position of the flites. Once the flites are 'aligned' there will be some distance relationship between the flite sensor triggers. Your job will be to keep this distance the correct value. You can probably do this by making a single triangular speed correction once you know the error distance.
That's why I said you probably don't need a specific homing function. Just run the conveyors normally and they will very quickly become aligned based on normal control.
The PowerFlex family will probably be able to do what you want depending on the version (4, 40, 70, 700, 700S). As you go up that list the capability increases. I'm pretty sure the 70 and above will take an encoder input as a speed reference but I'm not convinced you would need to use an encoder reference.
As Leadfoot said, designate one of the conveyors as the master. This conveyor just gets a raw speed reference with no correction. The other conveyor gets the same raw speed reference (scaled to get the correct surface speed) but also gets the correction to align the flites.
I'm pretty close geographically. As you get going on this I may be able to help if you get hung up.
Keith