Hey everyone 
I ran into the collection renaming problem one too many times and finally decided to do something about it. Just released directus-extension-safe-rename — it lets you rename collections and fields straight from the UI and handles all the system table updates automatically in one atomic transaction.
It covers relations, permissions, presets, flows — pretty much everything. PostgreSQL tested, other DBs still untested (help welcome! 
)
What gets updated automatically:
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Collections & fields metadata
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Relations (O2M, M2M, M2A)
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Permissions & presets
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Flows & operations & more
Install via Directus Marketplace or npm:
npm install @contensu/directus-extension-safe-rename
NPM: https://www.npmjs.com/package/@contensu/directus-extension-safe-rename 
GitHub: https://github.com/contensu/directus-extension-safe-rename
Still in beta so please backup your DB before using 
Feedback and bug reports are super welcome — especially from anyone running MySQL, SQLite, or CockroachDB. Happy to answer any questions!