Hello Marko,
1 / If you stretch a beam on the side where you have the holes, yes the holes are also moved / stretched (which is not the case for the holes on the opposite side of the beam)
2 / I recommand you to use the "Advanced Trim/Extend" command (if you are using Advance Steel on its own CAD platform, you can find the icon in the Tool palette > Tools (then scroll down with middle button of your mouse) - see attached picture)
Best regards / Philippe
Attachment: Advance Steel - Advanced Trim - Extend.jpg