You can run the query from the Atlassian Database Schema page to see if the data is still there:
select * from customfieldvalue where customfield=(select ID from customfield where cfname='YourFieldName');
From my testing, if I delete a value the data is immediately gone from the database so if you do find it there the first step is going to be to perform a full re-index so you'll need to schedule a maintenance period.
If you do not find the values in the database you'll need to restore from the last backup. I would also recommend opening a support ticket so the Support team can take a look at the logs and help identify what may have happened to cause this behavior and how to prevent it again in the future.
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