Okay, I figured this out.
In order to keep an overridden custom ini file from being deleted after it’s loaded, you either have to have ‘User’ as part of the config name (i.e. instead of UCLASS(BlueprintType, Config=“ClassConfig”) it should be UCLASS(BlueprintType, Config=“UserClassConfig”)), or you have to put
[SectionsToSave]
bCanSaveAllSections=true
in the Base or Default config.
Would’ve been super cool if this information were in the Config file documentation.