Are you talking about Microsoft 365 E1/E3 licenses or Office 365 E1/E3 licenses?
Sure, you can change the licenses without issues. You can compare the plans whether they still cover the features and storage limits that you need.
See: https://www.microsoft.com/en-us/microsoft-365/compare-microsoft-365-enterprise-plans
And: https://www.microsoft.com/en-us/microsoft-365/enterprise/compare-office-365-plans
When it comes to mailboxes, you can also convert it into a Shared Mailbox without the need for a license (as long as it is <50GB) or assign an Exchange Online P1/P2 license.
See: https://www.microsoft.com/en-us/microsoft-365/exchange/compare-microsoft-exchange-online-plans
Similar plans exist for OneDrive for Business in case you only need to maintain that (or converted the mailbox to a Shared Mailbox).