since today (didn't play the last 2 days) I can no longer adjust the miniloaders (chute and miniloaders) pickup with bobs adjustable inserters.

This was an intended balance change in Miniloaders v1.6.8, which came out more than 18 months ago.

I don't know why but even in the latest version I can /cheat and configure them with the adjustable inserter GUI and they operate in all kinds of bizarre ways. I'm 13 days in a playthrough with a partner and suddenly it stopped working after my friend had been using that feature. How in the world was it enabled for 13 days? I did "accidentally" updated the mod from 1.11.3 to 1.12.1 and even when I choose the old version to run, none of my saves (even ones I never loaded with the new mod installed) will work, but yet /cheat in a new game allows the configs but /cheat in the 13 days old game does not.

Based on your answer we will probably migrate old loaders to be more simple in their usage as you recommend for balance, but I am still perplexed how/why this all happened when the version we used was so much later than 1.6.8.

It looks like there's a bug where Bob's Inserters isn't getting disabled for miniloaders on a fresh new game, but is disabled if any of the mods in the save are updated. Very strange.

Is there any way to enable bob's inserters again? My entire game is broken as we used miniloaders for just about everything, then updated a mod.

Figured it out. Commented out line 76 in Control.lua register_bobs_blacklist()
This would be nice to have as an option in the mod.

Unfortunately it's not quite that simple, because miniloaders are several inserters stacked on top of each other in the same map tile. Bob's Adjustable Inserters might adjust the pickup/dropoff points for all of them together, or it might not. It has caused bugs in the past, which is part of the reason it was disabled, in addition to the balance concerns.