I am unaware of any hard and fast rule either, but having thought about it and looked at some NGram results showing actual uses, a pattern seemed to emerge.
Help with is used for a concrete thing. Saying "in" in this context would not make sense:
I will help you with your program.
This will help you with your skin problem.
Help in is often used when there's a verb involved. Saying "with" in this context probably works in most cases but doesn't feel as natural:
I will help you in writing your program.
This will help you in curing your skin problem.
Help in is also used when the thing in question is more nebulous/abstract. Saying "with" makes sense in the first two examples but not the third, so I'm not sure if there's a general rule here:
This will help you in life's journey.
This book will help you in a number of areas.
I will help you in every way I can.
https://english.stackexchange.com/questions/59918/help-somebody-with-vs-help-somebody-in