"Only" here is somewhat implicative of "every" in this particular usage (although some might disagree with my interpretation of that) but in general the mean two different things.
Consider a more simple case, where you say something like one of these.
a) Every man is tall.
b) Only men are tall.
As you may or may not notice, there's a pretty significant difference here. In the first, we're saying that if a person is a man, he must be tall. We're disregarding the truthfulness because neither of these statements is actually true, but that's what that statement would mean. On the other hand, the other statement is something of the inverse: if a person is tall, he must be a man. From a purely logical standpoint, neither implies the other. You would have to say something to the effect of "every man is tall and only men are tall," if you wanted to suggest that both are true.
The word "only" is saying that only elements in the described set may match the attribute given, whereas the word "every" is simply indicating that each element in that set does display that attribute.
Fundamentally, "every" is limiting the elements in that set (in this example, "men"), and "only" is limiting the elements outside that set.
Moving back to what you actually asked about, then, the same difference applies.
Only what contains Omega 3 is fish oil.
If you were to replace "only" with "every" (and there are some grammatical errors with doing that as you have, but those are minor and I'll address them later on), you would be changing the meaning. Right now, it's saying that nothing is fish oil, unless it contains Omega 3. If you changed it to "Everything that contains Omega 3 is fish oil," you would be altering the meaning to suggest that something cannot contain Omega 3 unless it is fish oil.
I'm not sure if I've explained this particularly well, but I hope my example helped. Let me know if I can clear anything up. It's actually a fairly complex matter in logical reasoning, and there are college classes that go over these sorts of differences.
I promised a bit on grammar, so here it is. I won't get into detail, just what it should be.
Every fish oil contains Omega 3. Every foods that contain Omega 3 help with brain development.
But technically, this would have been the correct transformation:
All fish oil contains Omega 3. Every food that contains Omega 3 helps with brain development.