Renaming a Content Type Machine Name
It is impossible to tell whether you've missed something without having complete access to your schema.  The fact that you get an entityreference error after clearing all caches is not a good sign.

A safer approach to renaming a content type machine name is to recreate the bundle with the correct machine name, and then use Node convert to convert it from the old machine name to the new one.


  Node Convert ... gives the ability of converting the node from its current node type to another node type. Also it gives the ability of transfering all the custom CCK field values of the current node type to the destination CCK fields, or discard them. As of 5.x-1.4 you can bulk convert many nodes of the same type, to another one that can be accessed in Administer → Content → Convert Nodes.


It allows both single node a and multiple node conversion. Here is a link to the documentation.

I've used the module for a similar use case as yours, with success.