Hello @DeanHowell1 ,
The web map JSON determines which portal items are consumed in the web map. Can you confirm if the items that should be in the web map still exist in portal? I would also recommend taking a look at item ownership and sharing for missing items.
You can also use a tool called ArcGIS Online assistance to view the web map item JSON.
We don't support this tool directly and I would recommend caution if you plan to make any changes the web map JSON directly. That said it may help you determine why the web map is missing content.