Considerations for Employee Absence
Are you considering treating his absence from 13.6.20 till 1.7.20 as leave and pay, or treating the period as absent/LWP? Taking a lenient view, if there was at least oral information that he was unable to report for duty, you may consider debiting his leave account and settling the matter.
My view is, since he had not applied for any leave for this period until his death, you may treat the period as LWP and record 1.7.20 as the exit date to close the matter.
Options for Closure
On the other hand, if you treat the period as 'resigned or terminated,' you will have no records to prove this and must proceed according to the applicable procedure for closing the issue. This is not appropriate.
One more option is to close the matter as 'absconded' as of the last attendance marked, terminate him on record, and proceed further. With no other record, this is the only choice.