Kevin File extensions are quite arbitrary information that does not have any influence on how the data inside the file is actually structured. You can change the file extension to any other (for example ".mt940"), the contents of the actual file will still be the same.
That being said, if the software used by your bookkeeper is not able to process the MT940 file exported by bunq, it might have to do with the file extension, but it could also simply be caused by their software not able to parse the file contents correctly. Hard to say without having access to the software by yourself, but your bookkeeper should be able to explain it in more thorough detail.
There are also CSV formats available from bunq that certain software might be able to read as an alternative. These kinds of files however are less standardized and might require more manual work when importing.