You can prune the emails by using the 'Email Disk Usage' feature within cPanel; this feature allows the selection of specific emails, e.g. removal of emails that are older than one year. Please see examples in the cPanel screenshots below:
Selection on a date - emails deleted older than a year.
Selection of a sender (from) - emails deleted from a specific sender.
A few of the codes for the selection (Custom query) are listed below:
FROM string
Matches messages, which contain string in the FROM field of the message’s IMAP envelope structure.
CC string
Matches messages, which contain string in the CC field of the message’s IMAP envelope structure.
BCC string
Matches messages, which contain string in the BCC field of the message’s IMAP envelope structure.
SUBJECT string
Matches messages, which contain string in the SUBJECT field of the message’s IMAP envelope structure.
TEXT string
Matches messages, which contain string in the message headers or body.