Keeping emails as reference on a mobile device is not a good solution. Of course, you're free to do what you wish, but just be aware that you're living dangerously by doing that - as a user, I would not recommend that.
The best solution : create a folder on server side to save those important messages, AND use Imap mode.
I took this a different approach for my own. Years back I set up my main email account to forward all incoming emails to another account. This secondary account is configured on the phone (imap). This way, should something happen where I delete an important email by accident or the email app has an issue, my desktop's email access is completely isolated from the phone.
My PC pulls in emails using pop3. Only the last 2 months of emails for the primary account are stored on the server. As for the secondary account (on the phone), once viewed, unimportant emails are immediately deleted. Every so often I'll log into webmail for this account and clear out everything else, keeping again the last 2 months or so on the server.
This strategy has worked well because most (99.9%) of emails are never replied to. If I absolutely have to reply to something, I'll bcc myself so I have a record of the response on my mail account. This whole solution may not be the most efficient, but it provides some level of redundancy.
Another benefit, should the phone ever be lost/stolen, I can disable the forwarding, login to webmail to delete all messages on the secondary account without affecting anything on the primary. As soon as the lost/stolen phone is connected to data, all messages are erased as a result of imap syncing.
