Sooner or later they would have found out how important the towers were.
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The problem for the Germans was that by the time they found out about the RADAR towers, the Allies had ENIGMA....which, by the way, was turned over by the Poles to the French who turned it over to the Brits. Probably the best kept secret in world history was the Germans not knowing we had ENIGMA.
“Similarly, Ultra’s role in the Battle of Britain was limited: better grade intelligence came from prisoners, captured documents and improved air reconnaissance.” p I didn’t think that Enigma had much of a role in BoB or later air campaign.