A bit of background:

I have a site with a lot of nodes.

I had created a new doctype that had 1 node instance created.

I renamed that document types alias. This operation did not finish after 20 minutes, so I decided to do an iis reset.

After that I started getting YSOD errors from the examine indexing when I published content. So I did the following:

Delete the content instance of the doctype. Empty recycle bin. Delete doctype. Delete Examine Index files. IIS reset.

Now I could publish content again. Problem now is that the umbraco.config file is almost empty. When I publish my top node, that node gets written to the file. If I delete the file, and IIS reset, then the file is regenerated, but still only with one node. If I publish the a top node, with all children, then those children appear as well. 

I have a lot of top level nodes, so I'd prefer not haveing to publish all of them with children. What could be going wrong here? What does a doctype renaming actually do? Does it clear all the xml cached content in the db or what? Something must be missing from the DB since it cannot create an xml file that correctly reflects the state of the content?

EDIT: The nodes that are not in the cache file, also seem to be missing from the cmsContentXml table. Is there a quick way to regenerate that table?

EDIT 2: Umbraco version is 4.9.2