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SS-A
is the System Loads Summary: it gives you the monthly sum of energy for heating/cooling as well as the monthly peak for your system based on the weather file you have.
It shows monthly cooling, heating and electrical loads. The loads shown are the sum of zone-level loads and central air-handling-unit loads
SV-A
is the System Design Parameters: this report echoes your input to the program for each system as interpreted by the SYSTEMS design routines
Source: DOE22 Volume 4 Libraries, page 134 (140 of PDF) for SS-A and page 124 (130 of PDF) for SV-A
The fact that the values in SS-A would indeed be reduced makes sense, since this is the actual monthly heating/cooling loads, and you have some pre-cooling done at the Primary Air Unit level.
As far as why you're not seeing a difference in SV-A, I can't tell from the information you provided, it's unclear whether you're autosizing and what are your inputs to it. The fact that you're not seeing a difference means that the system parameters - either entered manually or computed by eQuest - are the same.