In 2012 I purchased a BN Crane Car (L29885) and a Lionel Legacy Control System V1.4.  I played with the Crane using the Legacy System that I used in conjunction with an old ZW transformer for several months, but I started doing other projects and hobbies and had not used the system (or tried to use it) until several days ago.  What I discovered was that the batteries in the controller will not charge.  I even replaced the batteries with new rechargeable batteries, but still no charge.  I have let the charger attempt to charge the batteries for 24 hours at at time; no luck.  I replaced the batteries with alkaline batteries, but the hand-held controller had difficulty finding its base but ultimately did so.  I turned on the power to the track and the rear light of the crane lit, but I could not get it to do anything else.  Basically I have two questions: Why will the rechargeable batteries not charge? and Why will the crane not work other than the rear light?
Any help would be basically appreciated.  Thanks.

Welcome to the hobby.

Don't be afraid of looking silly or being a novice at the hobby shop.  They are likely to be glad to see you and will be helpful.  Their business depends on new as well as older customers.

Have fun.

Welcome back to the hobby.

What you have described about the engine when the whistle is blown seems odd to me.  I have engines that are much newer than 25 years old and none of them do as you describe when the whistle button is activated.  There must be something about your engine or the ZW transformer that is causing this to happen.  Do you have another transformer?  Do you have other engines with horn or whistle?  What type of reversing unit does the engine have?  I am curious about why this is happening to your engine.  Is there an O gauge club in your area or a Lionel service store?

IMHO the answer is no.  I do not think that the radio waves produced by your legacy control system would be able to throw the switches due to no receiver in the 022 switches.