had this problem as well:
no elements are actually being deleted and the number of elements that archiCAD says is related to the number of objects with "bad parameters" on screen at startup.
you will probably notice big black dots on your plan that usually represent missing library parts? these are the 'deleted' elements.
simply select them and change the parameters around a bit until you can get them to display in the preview window. all should be well again, albeit another unnecessary "upgrade" issue fromGS.
(FYI - my issues were with curtain walling objects showing 'first panel' as 'on')
HTH
~/archiben
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