Hi Markus,
from what I understood, you want to identify the issues which got flagged two days ago. Not those were flagged previously and were still flagged, but those who changed on this day from unflagged to flagged i.e. the delta for this day only.
If this is correct, there isn't a easy way to do that. Neither JQL nor the Agile reports support that.
The only solution that I know is if you use Cycle Control and utilize the metrics module - it keeps track into the changes for each configured JQL on a daily basis and can show you what got flagged and what got unflagged. If this is the only thing you need to accomplish it might be overkill, but it is still an option.
This screenshot show how Cycle Control the changes in a metric for a single day - in this case 207 new unresolved bugs came up, in your case this will be flagged issues.
image2016-6-16 14:55:52.png
I hope this helps.
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