You can't save a database to the same file it was read from, because it may not have been completely read in initially, so saving to the same file poses the risk of concurrently reading/writing to the same file.
The SAVE command uses saveAs() to save to a different (e.g., temporary) file and then either deletes or renames the original to *.bak, and then renames the saved file to the original filename.
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I know nothing about ObjectArx, but in other languages you have to use the SaveAs method, and not the Save method. It is a bug in the their code as far as I know.