You shouldn't try to simply concatenate them in time because there will be a discontinuity between the end of the first dataset and the beginning of the second dataset. What you can do, if you're using fieldtrip, is to append them as two different trials (it's ok if they're different length).
Use the function ft_appenddata() to do this. It has different behaviour depending on if the channels between the two datasets are the same or not. If you need to save them back to their native file formats, you can then use ft_write_data() to do this.
