I've set up hundreds of pages, many of them using separate designs and design customisations.
I'm now going back to set up the printer friendly design. To do this, I've clicked on Setting for the Site and pointed to the printer friendly design I've created. However, I haven't committed this change because I'm paranoid that the front end design (which I've also just changed, but haven't committed, in an attempt to influence newly created sub assets) which is applied to the Site will now cascade through all the sub assets, overriding hours of work.
Is this what would happen?
It wouldn't happen – a design cascade won't override specific designs set at a lower level.
However, for a printer-friendly design, you want to add a User-defined design instead. That way, you can call a page with that design specifically. To do this, lock the settings page at the site level, provide a design code (e.g. "printer") and then select the design. This then adds an additional design to all the pages.
You can then create a link to this design by using the following code in your parsefile:
[html]<a href="<MySource_PRINT id_name="global" var="asset_link" start_query_string="true" append_query_string="true" />SQ_DESIGN_NAME=printer" target="_blank" title="Printer Friendly Version">Printer Friendly version</a>[/html]
The value for SQ_DESIGN_NAME must match the design code you provided when you applied the design.
Hope that makes sense!
Phew! Thanks for clarifying that.
The method you described for the user defined design is what I was trying to do. Now I'll just keep my fingers crossed…
Did you remember to make a backup of your installation before you started? 
Just a note (as it caught me out the first time) - the name you put in for the User Defined Design is converted to lowercase so it'll need to be referenced in lower case in the parse file.