Today we changed the SSL settings in Cloudflare from Flexible to Full (strict) and in about an hour our website got flagged by Google for phishing, resulting in the website getting a red warning screen, mail being blocked and the website not being indexed anymore.
Changing it back didn’t help ofcourse because it was already flagged. My question is why is this happening and is there a way to prevent this from happening ever again?
That has nothing to do with your encryption mode, which should always be Full Strict.
Maybe it’s not the root cause but could it be that the change set something in motion by Google?
Im just trying to understand the process because within an hour after the change we got flagged, or would that be just coincedental? 
That is absolutely coincidental and unrelated.
Make sure you are on Full Strict and follow the steps provided by Google to get your site unlisted again.
The only way this could be remotely related is if your server was not properly configured and served different content for HTTP and HTTPS.
If your server serves questionable content on HTTPS, then Google may have listed it because of that, but that’s an intrinsic security issue with your site and needs to be fixed by your web developer.
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