Lists in Scrivener are a known and acknowledged problem. They do not work well and can not survive even the most routine editing. Other than taking a “set it and forget it” approach to a list where you create it and never reorder the items, the best advice it to either avoid them, use markdown instead, or “treat them as unstable dynamite when editing around them.”
See these threads, among others:
Inconsistent formatting and indentation for hierarchical ordered / unordered / bullet lists