When upgrading a users email license from an E2 to and E3 license, their mailbox storage should increade from 50gb to 100gb. Sometimes this will refuse to sync up with Exchange causing them to still be limited at 50gb. The issue lies with Microsoft, and I have submitted feedback to them to fix it. In the meantime, PowerShell can be used to force the change.
Open Windows PowerShell as an Administrator
Run command "Connect-ExchangeOnline"
Run Command "Set-Mailbox user@impactlife.org -ProhibitSendQuota 98GB -ProhibitSendReceiveQuota 99GB -IssueWarningQuota 94GB
Check mailbox size again.