The number of entries in the channel file (in the .Channel field) must correspond to the number of signals in the recordings. The name and type of channels in the channel file created might be incorrect, but the number of channels should always be correct.
You should not try to add or remove channels manually, especially when working with continuous files, which can't be edited from Brainstorm.
If there is something that obviously crashes even when you don't modify the channel file: could you please share a short example file? Upload your files somewhere and post the download link here.
If you can, please extract only one second instead of sending the entire recording session. Then make sure the error can be reproduced with this short file.