Its quite alright to be new to inventor but the problem you have can be solved albeit slightly mundane.
1. Open up the parts file for the chassis rail in its normal drawing (not as an assembly)
2. right click one of the flat, long faces of it (IE, not the end, though it can be done, lets keep it simple =D )
3. click "start sketch" (or some similar command, it depends on your inventor version)
4. Draw a simple box over the section you want to cut off, be aware that you keep your spacing as autodesk does EXACTLY what you tell it to, so you might need to cut off 9.5 or 10.5 inches to get the holes lined up properly.
5. Finish the sketch to enter into the modeling commands.
6. Click Extrude and select your square, use an appropriate depth to get rid of the bar entirely.
7. Before you click through on the extrude click the second box under the section where you put in your depth, this should tell it to subtract rather then add. Youll know you did this right if the outline of your box is in red as you look at it from an angle.
8. Click okay and voila! your C-channel has been cut
9. go to file, Save as.. and save it as a DIFFERENT file, IE C-channel_short_bar *
* the name doesnt matter, but it MUST be different or else you just changed the original part and will have to re download it from FIRST or your parts backup.
10. Rebuild/re-mate your assembly with your new part.
Hope i helped!!