I've had the exact same issue just yesterday. I'm using Revolution 2.3.1.
On a new site that I'm creating I had a single document resource ('Home': ID 1) and then added an Articles resource ('Blog', ID 2), to which I added a couple of articles (IDs 3 and 4). Later I added three new document resources ('About Us': ID 5, 'Services': ID 6 and 'Careers': ID 7) and as I wanted the blog to appear last on the live site menu I changed the menuindex for it to be 8. At that point, the services and careers resources disappeared from the resource tree in the manager. I could still edit the resources by manipulating the edit URL for a resource that hadn't disappeared.
To try and get round this I tried deleting and readding the two resources but to no avail - they still wouldn't appear. I also tried toggling both the publish and hide from menu options for the resources, and setting the menuindex for the blog to an even higher value (20) but they still failed to appear.
Following Bob's advice earlier in this thread I examined modx_site_content
select id, parent, menuindex, pagetitle from modx_site_content;
to check the parentage of the missing resources and they correctly had 0 as their parent resource.
By now I had resource IDs up to 10 due to deleting (also using 'Remove deleted resources' to purge the deleted resources) and readding, so I decided to try changing the IDs of the resources directly in the database.
I changed the IDs for resources 9 and 10 (the recreated services and careers resources) to be 3 and 4 (the IDs I had for those resources before I deleted them) and then changed the ID for the blog from 2 to 10. I then flushed the cache and refreshed the resource tree in the manager and hey presto, all of the resources now appear.