myAnnot.CreateEmptyAppearance(AppearanceStreamModes.Normal);
...
myAnnot.NormalAppearance.Add(...);
...
myAnnot.GenerateAppearance(AppearanceStreamModes.Normal); // This creates several object resources in the PdfIndirectList and PdfCrossReferenceTable.

page.Annots.Add(myAnnot);

page.Annots.remove(myAnnot);

            //Get a cross-reference table and a list of indirect objects in the document 
            var list = PdfIndirectList.FromPdfDocument(document);
            var cross = PdfCrossReferenceTable.FromPdfDocument(document);

            //Receive a list of objects that have at least one reference in the document
            var refObjects = PdfRefObjectsCollection.FromPdfDocument(document);

            var objectsToRemove = new List<int>();
            foreach( var item in list)
            {
                if ( refObjects.FirstOrDefault(a=>a.ObjectNumber == item.ObjectNumber) == null )
                    objectsToRemove.Add(item.ObjectNumber);
            }

            foreach (var objectNumber in objectsToRemove)
                list.Remove(objectNumber);

            objectsToRemove = new List<int>();
            foreach (var item in cross)
            {
                if (refObjects.FirstOrDefault(a => a.ObjectNumber == item.ObjectNumber) == null)
                    objectsToRemove.Add(item.ObjectNumber);
            }

            foreach (var objectNumber in objectsToRemove)
                cross.Remove(objectNumber);