Mail is not directly synchronised between devices; instead, your devices will synchronise via the Mail server that hosts your email account(s). Are you using an IMAP or POP3 mailbox? If one of your devices is using POP3, this can cause problems with keeping Mail clients in-sync.
Deleting and re-adding your email account - from one or potentially both devices - is sometimes the easiest way to resolve a problem with a specific Mail account. After deleting the account, perform a forced restart before re-adding the email account to your device:
Settings > Mail > Accounts > [Your Mail Account] > Delete Account
Force restart iPad - Apple Support
Force restart iPhone - Apple Support
Settings > Mail > Add Account