Your solar charging system is a totally separate system, and should NOT have been wired to the battery disconnect switch. Also, there should be a fuse for the solar close to the battery connections.
The battery disconnect is to prevent DRAIN on the batteries... not to prevent "charging". However, depends on who wired it...
Long story short... If wired CORRECTLY, the battery disconnect doesn't affect the current coming from your solar panels going into your batteries. I recommend leaving it OFF while in storage to prevent parasitic drains on your house batteries.
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