This isn't really a legal question; however, let me answer with a question: what do you think the odds are that they'll find out about the investigation of your former employer? Perhaps more to the point, what do you think will happen to your clearance if you don't tell them about the investigation and they end up finding out about it anyway? I'm going to guess that the odds of getting your security clearance under those conditions are rather small.
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Probably, but to receive any realistically accurate answer you should ask a Canadian licensed attorney.
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