If I have a mod like for example, The Lost Spires, and say I have played some of the way through it.
Say also that it turns out that I would like to upgrade it to the latest version.

If I do a clean save, I will wipe out my progress in the mod, yes?
meaning that I will then have to start again from the beginning.
This is correct isn't it...?

Yes, if you did a clean save you would wipe out your progress, however you should only need to do a clean save if you are specifically directed to by the mod author.