Is there a chance with .xlsx to let phpexcel write into sheet 1 without "hurting" sheet2? So sheet2 can contain OLE objects, charts and load the (input) data from sheet 1.
At present PHPExcel does not support either OLE objects or charts, although I'm working to implement charts for the next release. So currently, the answer is "No"
If not: Can 2 .xlsx documents be merged together to finally have the expecteded solution of sheet 1+2 where #2 is not filtered or cleared for unknown objects?
The answer to this is "No"... you'd need to find an alternative utility to do this.