You can remove annotations with an SDK Script in Workflow.

Note that this would remove all annotations, including stamps and such, but it doesn't take much to add checks so it would only remove specific types of annotations.

            bool removed = false;

            try {
                // get document
                using (DocumentInfo doc = (DocumentInfo)this.BoundEntryInfo){
                    // iterate and remove annotations
                    foreach(AnnotationBase ann in doc.GetAnnotations()){
                        // delete annotation
                        Annotation.Delete(ann.EntryId,ann.PageNumber,ann.ItemId,RASession);
                    }

                    // save changes
                    doc.Save();

                    // set success
                    removed = true;
                }
            }
            finally {
                // set results
                SetTokenValue("Removed",removed);
            }

The try-finally is there to catch errors and ensure the output token is set.

In the Workflow, you pass the target entry as the Script's Default Entry, so in your example you'd put it inside the For Entry loop and pass it the Current Entry.

Then, after it runs you can check the "Removed" token to make sure it worked before moving on to the next step, retrying, etc.

On a side note, if your Move Entry is meant to move each document rather than the whole folder, make sure it is inside the loop and also targeting the Current Entry.