This is a caching problem.
Can you check when you reproduce the error to clear the cache (if yo can recycle the application pool that will clear all cache) and log with the same user again. By logging the different user the current cache is invalidated and the update of the database is reflected in the backend UI.
Another way is to make an update to the sf_taxonomies_table (any update to the table will be sufficient)
using the taxonomies API
to query some data change something in the taxonomies table and call .SaveChanges(); to commit new transaction to this table. In the code below I add new tag to a blog post which will update the taxonomies table and the error will be gone.
var taxManager = TaxonomyManager.GetManager();
var taxon = taxManager.GetTaxa<FlatTaxon>().Where(t => t.Name ==
BlogsManager blogsManager = BlogsManager.GetManager();
var myPost = blogsManager.GetBlogPosts().Where(d => d.Title ==
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