I think Alain Maashe from this thread: http://community.logos.com/forums/t/3238.aspx?PageIndex=3 may be right about the "credits" to your upgrade price
based on resources you have purchased being very heavily cut. If you
paid $120 for BDAG you don't get $120 credited to your upgrade price,
you get some small percentage of your original purchase price credited,
maybe something like 10% (think total upgrade price divided by MSRP for
all new resources in the package). So, while Logos can honestly say
you "never have to buy a resource twice", you may only be getting less
than a dime on every real dollar you spent on separate resource unlocks
applied against the upgrade price.
If this is really how the
upgrade calculator works, the question is would you rather sell your
Pillar Commentary or Baker Commentary set at a 50% loss on ebay (I don't know what you could
get for it by selling it separately so 50% is just a guess) or get the
"dime on the dollar" or whatever percent the resources are marked down
through the logos.com upgrade calculator.
If the calculator
does work this way you would always be better off to sell your separately purchased resources on ebay and apply your earnings to the upgrade.