If a SAR was filed, and during the 90 day timeframe afterwards, we learned that the bank suffered the loss, do we mark the next SAR as an amendment or a continuation? It is past the 90 days, we took a loss which was not reported in the first SAR, but there has been no additional suspicious activity aside from us confirming we took the loss.

Why not just a corrected SAR?

If you have suspicious activity that warrants a second SAR at this point, just include the statement of loss there. I wouldn't advise filing a continuation SAR just to report a loss, I would just amend the first. I would also file a local police report if the bank is a victim and the situation warrants it.