You might have reached this page from an article on the Australian Coroners Court hearing.
I suggest to read this post for more information first.
That post will explain that John Helmer writes a lot of nonsense on MH17. The website you are reading now is the only one with no agenda.
The forward pressure bulkhead of MH17 was recovered from the crash site. According the DSB final report (page 63) three holes were visible.
Wreckage was at arrival in Gilze Rijen first photographed and registered. When it was photographed there is a single big hole visible. See page 63 of the english report and page 68 of the Dutch report.
However at the 3D reconstruction shown at October 13 an additional hole could be seen. It is unclear what caused this additional hole.
However it is likely the hole was made by DSB staff to be able to attach the bulkhead to the frame as photos below indicate.
Appendix Y explains the lower hole is caused by airplane parts pushed through the bulkhead. See image below.
DSB writes in the final report there is a risk of damaging the wreckage when it is being attached to the frame.