Indeed, the Hardy Boys fan does face a dilemma. The Casefiles tell us that Iola Morton was killed by a car bomb, but in the Mystery Stories, Iola is alive and well. What's the truth? Well, I can come up with three ways to rationalize this:
Explanation #1: Frank and Joe are undeniably older and more mature in the Casefiles. Witness the evidence: they carry guns, investigate murders, and deal with international crime more than ever before. So, we can argue that within the Hardy Boys universe, the stories told in the Casefiles series all occur after those of the Mystery Stories, even though Mystery Stories are still being released today. Never mind the publishing dates -- in time, the Casefiles occur after the Mystery Stories.
By this reasoning, it would seem that Iola really is dead. She's still alive in the Mystery Stories being published today because the events in the Casefiles haven't yet happened -- but they will.
Explanation #2: The Casefiles series was cancelled, but the Mystery Stories are still being written. Furthermore, the Mystery Stories are direct descendants of the original Hardy Boys books released in 1927. Because of this, the Mystery Stories are the final Hardy Boys authority, and if they say Iola is still alive, she is still alive, darn it! The events in the Casefiles should be considered apocryphal by true Hardy Boys fans.
Explanation #3: The Casefiles and the Mystery Stories take place in alternate universes, and have no bearing on each other. Casefiles Iola is dead, and will remain dead. Mystery Stories Iola is alive, and will remain alive. Both statements are true. The Casefiles and the Mystery Stories are two separate worlds, and they aren't intended to be consistent with each other.