To help consolidate the multiple lines that ended up in my inventory when 2.0 rolled out, I started working on my Standard common and uncommon cards. When I made changes to the inventory quantities (placing all quantities on lines with details and eliminating lines without details), the row for the affected card disappears from the Inventory screen when I have the Advanced Filter set.

I was using these filters:

Is Foil = False
Format = Standard
Rarity = Common, Uncommon

Example:

I had two lines for Battle Hymn: 
     one had Qty=7, TradeQty=0, AVR, NM, English;
     the other had Qty=0, TradeQty=5, and no other details.

I consolidated the lines into one: 
     Qty=7, TradeQty=3, AVR, NM, English.  
     I made no change to the third line (a foil copy) that was not 
     displayed in the main screen due to the filter.

As soon as I clicked Apply, all lines for Battle Hymn disappeared.

This happens whether or not the quantities match the numbers present before the consolidation (i.e., combining a "4,0" line with a "0,1" line into a "4,1" line yields the same results as the example above where the numbers went from "7,0" and "0,5" to "7,3").

Using Google Chrome Version 24.0.1312.52 m.

Thanks for reporting, looking into this, there seem to be some small issues with the foil filtering.