Is it possible in Acrobat 9 Pro to disable the 'Select Image' button (in the bottom toolbar) and the right edit window while in

While it would be possible to alter the behavior of a "Select Image" button by writing a custom navigator, there is no way to turn off Acrobat's side pane when editing a PDF Portfolio.

UVSAR: is the 'Select Image' button a part of the navigator? From other information I found in the bigging of this project I understood this button was a 'hard coded part' of Acrobat itself and not particularly a part of a navigator (file).

Do I have to build a totally custom navigator just to alter this single 'Select Image' behavior?

You could intercept the normal process and implement your own version within the Flex code, for example refusing to update an asset if there's already one loaded, but the API in Acrobat 9 is a lot harder to work with than in Acrobat X.

In Acrobat the concept of Edit mode for PDF portfolios assumes everything that can be changed can also be re-changed, so there are no "one time only" examples to call upon. You are using them in a way that wasn't really envisioned when Portfolios were conceived, where you want some aspects to become read-only while others remain editable - in which case the navigator has to implement those features and work out a way to do it that doesn't make creating the master copy too cumbersome (you could for example embed the image into the NAV as a static element on the stage, so there's nothing for the user to replace, but it'd mean a new NAV for every map).

You'll also need to consider the impact of Acrobat X on your workflow, as custom navigators built against the Acrobat 9 / Flex 3 SDK aren't going to work the same in Acrobat X. Although a lot of people are still using Acrobat 9 right now, it's a legacy product so any development time spent on it has a limited lifespan, and any code you write for A9 will be pretty useless for AX given the change in Flex versions.

I had a similar which was solved using a JavaScript on the "Doc will close" event :

this.dirty = false;

This prevent end users to be asked to save any change they made in my portfolios before closing…

I don't think that'll solve anything in this case as the OP's users need to make changes to the files within the Portfolio, but without permission to change the background image. Undirtying the file doesn't prevent someone from saving it after making an accidental alteration, it just turns off the prompt (and if you're intending them to change something between saves, that prompt is important to show).

With Templates in Acrobat X you can lock down the background without having to write any Flex code (by embedding the image into the SWF). Yes you'd need to compile a new SWF for every base document, but it's a trivial thing to do. Users would still be able to apply something else over the top, or in Acrobat Pro they could switch to another layout entirely (which of course kills anything you've done) - but they're less likely to do that "by accident".