One of the pros will be along shortly to give you some advice. Hoping all is well with your engine. Do you have a Racor style filter with the clear viewing bowl / thumb screw in addition to the onboard Etec filter?
This is the first year with a new Etec for me, but with my previous engines I changed my primary and secondary fuel / water seperator filters every year. It's just cheap insurance.
I'll most definitely be doing it with the Etec too.
Chances are there is more water in the fuel tank and it would be best to have a company pump it dry to make sure the water is removed.
If the water was an accumulation of phase-separated E-10 gasolie, the remaining fuel would have less octane than before because 10% of alcohol adds about 3 octane points. If the octane drops below 87 then your motor could suffer problems or damage.
Have your engine's fuel system flushed out also as phase-separated mixtures are very corrosive, especially ot the precision steel parts in the pump and injectors.
To help avoid future problems, install a boat mounted fuel-water separator to help protect more motor. One with a clear bowl, such as the popular Racor style, can show you if water again starts to accumulate in the fuel tank, and this time, before it reaches your motor.
"There is never just one thing wrong with a boat";
-- Travis McGee, main character in a book series by John D. McDonald
The factory recommends that a properly trained technician service your Johnson or Evinrude outboard motor. Should you elect to perform repairs yourself, use caution, common sense, and observe safety procedures in the vicinity of flammable liquids, around moving parts, near high-temperature components, and working with electrical or ignition systems.
The information offered here is only general in nature and should not be construed as complete factory approved procedures, techniques, or specifications. Always use the proper service manual for your motor, up-to-date service literature, the correct tools, and have an understanding of how to proceed with troubleshooting and repair methods. If you are unsure or uncomfortable with a procedure, a situation, or a technique, enlist the services of a factory trained technician.