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When you disable the devel module it will attempt to restore the smtp library setting by copying the value of the devel_old_smtp_library variable into the smtp_library variable.
However the devel_old_smtp_library variable is only set when you visit the devel module's settings page. If you disable the module without ever visiting the settings page it will just blank your current smtp_library value since devel_old_smtp_library doesn't exist.
Either devel_old_smtp_library should be set when you enable the module or the disable should be a bit more discerning about what it actually changes.