Back in the Urgent security advisory, it was said that upgrading your RouterOS version would remove “the bad files” on the device.
I have not heard anywhere that this is not the case for all RouterOS upgrades, so I would assume that it remove all unknown files when upgrading even now.
While a confirmation from MikroTik would be nice, I see no need to panic before otherwise is proven. Not like I can do much about it until then anyway.
Just upgrade your routers to RouterOS bugfix >6.40.8 or stable >6.42.1, and possibly secure your routers. Once that is done, just wait for further information.
http://forum.mikrotik.com/t/urgent-security-advisory/117944/1