On db migration, migrations files are auto deleted v2.33.1

### Version Information

Server Version: 2.33.1
CLI Version (for CLI related issue):

### Environment

Macos 13.5.1 (22G90)

### What is the current behaviour?
When I do a migration (modifying my database or adding permission), the migrations files are created and then immediately removed as you can see on the video.

I switched back to hasura 2.27.0 (cli and docker) and I don't have the issue anymore. I add issue on 2.32.1 too

### Screenshots or Screencast

https://github.com/hasura/graphql-engine/assets/216573/8c47371a-8251-41a0-9795-98b291cebc78

### Please provide any traces or logs that could help here.

### Any possible solutions/workarounds you're aware of?

### Keywords

Reproduce the migration workflow with Hasura 2.33.1 using the CLI and Docker, then compare it with 2.27.0 where the issue does not occur. Trace where generated migration files are removed and consider the issue resolved when migrations remain available after database or permission changes.

Written by the indexing model from the issue text.