Have you tried to replicate the issue? Have you checked recycle bin?

To create notes in Lightning Experience, you must use Notes.

To set up Notes, add the Notes related list to all relevant page layouts and enable Notes.

You can have both note-taking tools enabled at the same time in Salesforce. However, notes can only be read and edited using the tool they were created with.

If done all that and still issue persist,You should create a case with Salesforce Support .