Hi antony_burnham
When you save an iolite v4 session file (.io4 file) it saves all the reference materials into the file. That way, if you send the file to someone else, the values used for the reference materials are included in the file. This helps avoid issues where someone says "When I crunch the data I get different values" because one person has changed the values in the file. It also makes it easier if are missing an RM file, you can easily create one from the session file.
So, to answer your questions"
1/ iolite saves the values of all RMs in iolite at the time of save, not just those used in the experiment. If you don't need that RM, you can ignore it.
2/ Import Once means that iolite will create a temporary RM for that file to use in the current session only. This can be really handy when testing out data from someone else without messing up the values you are using. Import Permanently means to update and change the values in your RM file. You may want to do this to update your local RM files if you've changed them in some way.
And of course, you can choose which files to change, or you can ignore this message entirely by clicking the cancel button. But it will show you this message so that you're aware the session you're looking at may have been created with different RM values.
I hope that makes sense, and if you have any questions, please let us know.
-Bence