I can't say as there is actually a drop dead easy way.
Let me see if I understand exactly what you want.
You want to run an LP query against the IIS log files to find out "active" pages, then you want to run another LP query against the FS input format to find files that are not in that "active" pages list?
Because of the limitations in the current version of LP of not being about to do subqueries against different input formats (e.g. can't query FROM FS with a subquery that queries FROM IIS), you'll have to do some magic to get the list of active pages into your second query.
I'd suggest using the TPL query generation method I documented in the General Discussion forum a while back. The first IIS query will output a list of the file names into a TPL format that is actually writing a new query that contains a where clause along the lines of:
WHERE FileName NOT IN (
'fn1.asp';
'fn2.asp';
'fn3.asp';
)
And then you run LP on that generated query.