If you are migrating and run the external-node importer, it should overwrite the class list for each host with the new information each time. (Instead, it combines them.)

Starting node info:

--- 
classes: 
  - base
  - class2
  - class3
  - class4
parameters: 
...

Run the import:external_nodes. Foreman shows (correctly) base, class2, class3, class4.
Edit the node in the external tool:

--- 
classes: 
  - base
  - class2
  - class5
parameters: 
...

(Remove class3, class4. Add class5.)
rake import:external_nodes again. Foreman will now show "base, class2, class3, class4, class5" - the removed classes do not go away.