In my experience you best don't bother with the tables in the database. Let Frappe keep track of this, don't interfere by dropping tables or altering tables.
Look at it like this:
If you are using a database system you don't bother what the database system does on the filesystem to organize itself.
If you are using Frappe you don't bother what Frappe does in the database system to organize itself.
When it comes to deploying your Doctypes on the next stage (QS, Production) you use "bench export-fixtures" to export and "bench migrate" to import your changes into your targeted Stage.
Don't create your own SQL-Scripts!