Not sure whether you are still monitoring this post, Jerry.
Anyway, here's some thoughts ventured ..

Conceptually, you should be able to achieve this via setting up a helper col
and then autofiltering on the helper.

Let's start by simplifying the scenario by having both sheets in a single
file. A simple 10 seconds copy n paste of say, sheet: B into a new sheet of
File A where you have a master sheet: A would do it. Rename this new sheet
as: B.  

In File A,

Assume that in your master sheet: A,
you have the key col (unique item#s for eg) listed in A2 down

In sheet: B,
assume the same key col is also col A, with item#s listed in A2 down

In sheet: A,

In an empty col to the right of data, say in col E,

Put in E2:
=IF(A2="","",IF(ISNUMBER(MATCH(A2,B!A:A,0)),"Y","X"))

Copy E2 down to the last expected row of data in the key col A. Col E will
check col A for blank cells & match each item in col A with what's within col
A in sheet: B.

You'd get 3 possible results in col E: blanks: "", "Y", "X". Blanks will be
returned where there's nothing in col A to be compared (this will flag
missing values in-between within col A, if any, and also allows us to extend
the check to beyond the current filled range in col A). "Y" would be returned
for items in A found in B, "X" otherwise.

Now you could just apply autofilter on col E (Select entire col E, click
Data > Filter > Autofilter), and select as desired from the autofilter
droplist in E1. If you want to "hide" rows in A which are not listed in B,
just select: "Y" (as you mentioned in your posting). If you want to "show"
rows in A which are not found in B, just select: "X".