Without effective stack filter the hand amount is the same. When I add effective stack is less than 40bbs the results and total hands are different between hem2 and hem3. 2046 hands -1,81bb/100 vs 2183 hands +2,08bb/100. Same hands same filters other than that "is hand playable" thing which you can not remove.
Hem3 filter is NumberOfPlayers >= 3 and EffectiveStackSizeInBBs <= 40.00 and IsHandPlayable=true
Hem2 filter is Number of players: From 3 to 10 Effective Stack in bbs is less than 40.0
Too much of hazzle for me to start sending you any hands, sorry. You can check it yourself if you or someone from your team has hem2 and hem3 + few hands played with different effective stacksizes.