It sounds like you CC3D was configured on OpenPilot firmware. The warning you saw were to advise you would change your firmware. So now it seems its on LibprePilot firmware - which is more up to date than OpenPilot which will never be updated again.
You will almost certainly have lost the PID and other configuration that was on your flight controller and you will now have either whatever you have tuned into the FC or whatever applied to your 250 quad from the options. From Memory - there is only one 250 setup on a 3s lipo - which I presume is what you have.
Transmitter and RX binding. I am guessing you have the flysky iA6 TX and a 6 or 8 channel RX. I am not sure of the binding process with that set up - BUT - I have the Turnigy i10 and use a number of the FlySky iA6 A RX. Binding them to my TX can be a frustrating event!
I run the binding process... the red light is steady on restart - indicting a successful bind. But the TX does not do anything to the quad!
I have to repeat the process time after time. What I do now is run the bind process - see a staedy red light in the RX... turn it off ( unplug battery) also now close the radio. then start radio - connect battery - try to start the motors. It works about 7 out of 10 times! last week I had this problem with a new RX.... in the end i gave up and went to regain my life with a wife and TV! Next morning came in to my "shack" - started the radio - plugged in a battery - fires it up and the motors started!
Word of advice: one of the most common errors with LibrePilot is - you have to remember to set the arming sequence and safe before disconnecting.
In LP, usal, bottom tabs - configuration - look for teh rdio icon and open it... top tabs - Arming Settings - the drop down menu will offer you choices - yaw right may be better suited - but you make a choice - save it and start the binding process.
I also suggest that your life will be less fraught and your flying much more thrilling.... if you spend some time going through the LibrePilot Manual online - if you look at some of the photo sequences which appear as slide shows - they can be downloaded as a PDF and easier to get at!
https://librepilot.atlassian.net/wiki/display/LPDOC/User+Manual
https://librepilot.atlassian.net/wiki/display/LPDOC/User+Manual
https://librepilot.atlassian.net/wiki/display/LPDOC/Multirotor+Wizard
Look at the bottom left of the slide show panel - a down pointing arrow underlined - click that to download a PDF which shows all the stages in the setup. Look at other similar pages and look for the download indicators...life gets easier!
Also ......
you have lost the presets Eachine use - so your PIDS may be suspect so be careful on start up. If you have problems - it may be that one of teh guys who has teh same eachine - can advise you on the PIDs etc,.
Hope that helps...