I think the autoflower nature will also help with the inbreeding issues, because as long as you’re breeding back to a new seed from the original packet, it will have at least slightly different genetics.
With photoperiod plants you can choose to breed back to the actual original first plant, but autos can’t do that for long.
I’ve managed one cross of progeny back to the original autoflower. With one of the auto strains that continues pistil production rather than senescing, focusing only on seed production, starting by fertilizing the preflowers, careful pruning with no fan leaf defoliation, and if I limited seed production numbers to maybe a dozen, and used cooler temperatures to slow down the plant in between seed sets, I’m pretty confident I could get 3 back crosses to the same exact autoflower. More would be very iffy.
I’m unlikely to do it though - by the time I’ve realized a particular plant is epic, it’s much too late to orchestrate that kind of plan. The single bx I did was decided late in the game, and with the plants to try it on only one Pine pulled through. I’ve noticed that the pineapple line I like will throw pistils and new growth for me for months beyond harvest. In contrast, some autos I’ve grown completely refused to produce new pistils and make seeds, even after a completely unpollinated life and 3/4 harvest of their buds. Those have been few, but also ridiculously frost-covered and potent.
I’m also unlikely to try a many times bx because my own breeding goal is toward genetic diversity. 
