Hello Michael,
To delete main table entry, which reference is used in any extension/child entity, we must define delete rule as 'Ignore' as mentioned in other answer.
Addition to above answer, Now if you are going to modify existing entity( delete rule for entity) you may face some issue, to accomplish this, you have to Cut and Paste your existing entity, modify delete rule and publish.
Another suggestion will be, instead of deleting record from entity, make it InActive for around 3-6 month data and archive older data.
Cheers,
Sanjay