Hi Danny,
The message limitation of a shared mailbox is 10GB now. From my understanding, you would like to reduce the size to 5GB as it used to be.
The following PowerShell cmdlet can be used to achieve this goal:
Set-Mailbox –Identity shared -IssueWarningQuota 4.5GB -ProhibitSendQuota 4.75GB -ProhibitSendReceiveQuota 5GB
This command set up 4.5GB as the mailbox size at which the user get a warning, 4.75GB at which emails cannot be sent, and 5GB at which emails cannot be sent and received.
Please note that this cmdlet can only be used to set up one mailbox. To reduce all the mailboxes size, I suggest you get assistance in our PowerShell TechNet Forum for the script to bulk-run this cmdlet.
Moreover, you may need this cmdlet to query all of the shared mailbox to write the script:
Get-Mailbox | Where-Object {$_.IsShared -eq "true" -and $_.DisplayName -ne "Discovery Search Mailbox"}
Thanks,
Henry Huang