I would import your CSV file twice… once into your “main” table, and once into a “comparison” table.
The main table MUST HAVE the unique ID as the first column (the primary field) in order for this to work properly. Otherwise, this will fail.
Before importing into the comparison table, delete all the records from the comparison table.
Then, in the comparison table, import your records, and make sure that you import the unique IDs into a linked record field that links to the main table.
Back in the main table, you will now have a reverse linked record field that will show you whether it has a match in the comparison table. If this field is empty, it doesn’t have a match so it can be deleted.
ALTERNATIVELY: Depending on how often you’re going to be doing this, you may want to consider using an external automation platform like Integromat. Then, as soon as a record is created/updated/deleted in your external platform, the exact same action can be taken immediately in Airtable (create/update/delete). No need to deal with imports at all.
Note that I am a professional Airtable consultant and a Registered Integromat Partner, and the Integromat link contains my personal referral code. If you have a budget for this project and you’d like to hire an expert to help you set this up, please feel free to contact me through my website at ScottWorld.com.