Hello Sander,

we (at Wolfram) are currently rewriting Import and Export of HDF5 files. Our goal is to add plenty of new functionality and to fix all existing bugs, including the problem you described.

Can you, please, provide the specific file that causes this problem? Or if it is inconvenient for you to upload it, can you at least provide a Matlab script you used to generate this huge dataset?

Thank you.

Dear Rafal, could you send me your wolfram emailaddress? You can find my email address either in the wolfram databases or on my websites. Even better would be a facebook/skype so we can chat.

Hello Markus,

as for now, we do not plan to extend our Import/Export functionality of HDF4 files.

I am aware that this is not a perfect solution, but you may try the following tool from the HDF Group: h4toh5 to convert your files to HDF5 format and then use Mathematica Import/Export functionality.