Well....that sounds unfortunate.
If you can't remove the transition, then either a) it's not the right transition, or b) you're in deeper than this trick will address.
OK, you want to try this, then?
Copy/paste the project into a new project.
Click on the timeline, ctrl-A (select all), ctrl-C (copy)
File/New Project
Click on timeline, ctrl-V (paste).
If you're lucky, the project will paste in and will work.
If you're NOT lucky, then clear out the new project (or create a NEW new project), and copy your original project in "chunks"
File/Open (open old project)
Select and copy a chunk from the timeline
File/Open (open new project)
Move scrubber to the end of the video on the timeline (if it isn't there already, like it will be when it's first opened) and paste
File/Save As (e.g. "myfile_1", "myfile_2", etc.)
File/Open (open old project) and repeat copying in "chunks" until you've populated the new project with as much of the timeline as will copy over easily.
What you've stumbled into is one of the reasons that in Studio, it's sometimes better to "work in chapters" -- make your video in sections, render each section out as a DV AVI file, and then make a final project that'll assemble those DV AVI files into final (e.g. DVD-ready) output. And don't forget to, every so often, do a "File/Save As" to save "checkpoints" to a new file (e.g. "myfile_chapter1_1", "myfile_chapter1_2") -- that way, if Studio eats your project (as it's trying to do to this one), you have a recent checkpoint to fall back to.
Good luck, and keep us informed of your (hopeful) progress.
BittMann