There are two proverbs I like, which perfectly apply to our IT world:
Refactoring is a high risk of damaging your graph by accident. It is possible to lose information by removing properties on nodes that have not had that information transformed. It also impacts the queries that you have already written for your applications. Hopefully, breaking changes will appear by running your unit tests, which I am sure you have written.
Performance may be impacted too, as shorter queries tend to execute more quickly; there is a cost to adding more relations in a query.