You should not mix UI and *.items files when it comes to the Semantic model - results are unpredictable.
If you want to maintain the *.items files then you will have to put all the Semantic model stuff into *.items files too. Make sure to delete the UI-generated Items first!
Note the last paragraph in the linked forum post:
If part of the Semantic Model was defined and created using the UI you may find that your stuff has lost its position in the model after a restart of openHAB. Recommend that it’s either all UI, or all configuration files, but not a mixture, to reduce unpredictability!