From what I'm getting from this, you're having an issue where once you enter a bonus room (by a pipe/door, whatever), it doesn't load in your bonus .lvl file?
I believe this is an easy fix:
Instead of making separate files, use sections. Sections are the numbers you see in the editor, and there are 20 total (+ 0)
If your 1-1 is on Section 0, then simply build your Bonus part on Section 1, then add the transport to it.
Sorry if I've misunderstood your problem, and if this doesn't help.