Forum Moderators: Robert Charlton & goodroi
changed around 200 links to my main site all in 1-2 days
My opinion - with that change you proved to Google that you have control over a multi-site network and will use it to try to improve rankings. Yes, I think you may well see some rolling trouble in the SERPs.
Google has both direct and secondary ways of monitoring this kind of thing. For example, they watch the churn in the SERPs to catch any urls that show sudden and dramatic upward movement. If their intentional algo changes don't explain the jump, they dig deeper and may throw "a flag on the play".
My course of action would be to try and get some seriously hi trust links to your homepage in an damage limitation attempt.