Best Practice for Managing Outdated Members in Transformation Rules?

This is really a matter of preference or ease of maintenance. Leaving redundant account maps in the Transformation Rules has no material impact as data related to those accounts will not be imported into OneStream anymore. You don't really need them for historical reporting purposes as you likely won't be loading historical data again and you don't need the transformation rules for any drill down capability as the historical datasets are already stored in the Stage tables. I would say the main reason for deleting them is if they are adding too much noise in the ongoing maintenance transformation rules due to the volume of redundant entries in the rule groups. If you are still circumspect about deleting entries you can always take an export of the relevant transformation rule groups prior to any mass deletion to provide a backup snapshot in case there was ever a need to rollback or reinstate certain mappings