Please understand that we're a small team based in Europe, emails coming in at 10pm at night are unlikely to get answered same-day unless it's some sort of emergency. You can generally expect to get an answer within 24h though
Anyway, I'll just answer here instead.
When you allow both flat calls and raises, you will split the range in two parts. Hands will either be played as flats or as raise (or a mix), whatever is more profitable for the hand. Since you are moving some hands from raising to flatting, the opponent's optimal response to your raise will also change. So even the hands that remain in the raising range will have a different EV, because the opponent will respond with a different range.
You can try manually locking the SB call-off range in the Advanced calculation to the same strategy as in the Basic calculation, then you should see the same EVs again.
Regarding green hands not being played: EVs / colors show the expected value of an action compared to folding. When you allow flat calls then there may be some hands that are +EV to raise compared to folding, but are even more +EV when flat calling. These hands will end up in the flat calling range, despite being shown in green in the raising range.
As always: Be careful with the flat calling lines, the calculation assumes a full check-down Postflop if the pot is not all-in pre.