I know what fixed the issue, but I cannot reproduce it to. When coming from the development repo we had this in the config.json file for one of of the reports that was going to be imported.
"tenantId": "avisonyoung",
"readPermissions": [
"655647240e547f0c8ce4ad55"
],
"editPermissions": [
"655647240e547f0c8ce4ad55"
],
"inheritedReadPermissions": [
"655647240e547f0c8ce4ad55"
],
"inheritedEditPermissions": [
"655647240e547f0c8ce4ad55"
],
"editPermissionsGroup": [
"65969a2c1b470b8f062b6eaa"
],
The tenantId and user/groupId did not exist on the instance that was being deployed to. As soon as this was removed, the issue not keeping the inherited permissions when away.
Sorry I cannot give more details.