What are your intentions? What is your level in the establishment? Are you in a position to make decisions, or can you only propose for consideration and approval? When did he join, and how many days has he actually worked?
Options Available to You
1. Close the matter and forget what has been paid and what is payable (if any).
2. To close the issue, you may consider following the necessary HR protocol:
i) Have you marked him present 'on quarantine'? Will you treat him as absent for the days not present to date?
ii) What about the probationary period compliance? No work, no pay? If so, he would be treated as 'not completed the probation satisfactorily' and therefore will be terminated.
iii) What did you do with the resignation he submitted? Did you process and approve it? I think you have not communicated your decision to him.
iv) If your terms of appointment permit 'one month' advance notice for resignation on either side and it's already one month over, accept the resignation and issue a relieving letter.
3. If you wish to recover the cash equivalent of the notice period not served (actual work), then you have to issue a letter to remit or serve and act accordingly.
4. I hope your unit has resumed normal work after the lockdown. If you don't want to accept his resignation, ask him to report immediately and decide thereafter depending on his response.
5. I think it's not worth taking all the efforts. Close the matter as "nothing payable/nothing recoverable." This is a practical solution suggested in the days of pandemic vagaries.