I noticed sometimes caseworkers are lenient with CSI if there are gaps, or it might be that they overlook things with the amount of applications they have to sift through. If it were me I would still apply anyway and try my luck. You could even do it yourself for £65.
You could get another 5-year residence card if you want to through form
EEA(FM). You could apply for PR confirmation again in December 2018, as long as you make sure to keep up CSI for everyone. You have to have permanent residence status for 1 year before you can apply for British citizenship.