• For all users this will change the warning email to 44GBs:
Get-Mailbox |Set-Mailbox -IssueWarningQuota 44gb
  • This will change the setting for one user (John Doe) to 44GBs 
Set-Mailbox -Identity "John Doe" -IssueWarningQuota 44gb
  • You can verify the setting on a user with the following command
Get-Mailbox -Identity "John Does" |fl

References 

https://community.spiceworks.com/topic/2143123-mailbox-size-warnings