Hi Stefano,
I bet that you would be able to use the WriteMetadata Method for an ENVI Raster. Here is a link to the documentation:
http://www.exelisvis.com/docs/enviras...
You can use ENVIRasterMetadata::UpdateItem to update a metadata item in the header or ENVIRasterMetadata::AddItem to add a new item to the metadata. The first link shows a good example of how this is used and you could probably extend this to a batch process by opening the files, updating the metadata, and then saving the header information.