Thanks Krzysztof Sienkiewicz
So in the end you have two IntraOrganizationConnectors and two OrganizationRelationships?
Are you doing something like this?
$or=Get-organizationrelationship "Name of the organization relationship created by hybrid" New-organizationrelationship -Name "O365 to On-premises2" -DomainNames "Remaining domains to be added separated by commas" -FreeBusyAccessEnabled:$true -FreeBusyAccessLevel "LimitedDetails" -DeliveryReportEnabled:$true -MailTipsAccessEnabled:$true -MailTipsAccessLevel All -PhotosEnabled:$true -ArchiveAccessEnabled:$true -TargetApplicationUri $or.TargetApplicationUri.OriginalString -TargetAutodiscoverEpr -$or.TargetAutodiscoverEpr.OriginalString