If a company is charged for these fees and goes to court but is subsequently found not guilty for the breach, can the company claim back the charges made by the HSE ?

I would say that FFI and prosecutions (I assume that this is what you mean by going to court) are essentially 2 'discrete' issues i.e. an action that involves a FFI wouldn't necessarily involve a subsequent prosecution, and I ideally that is something that the company involved would presumably want to avoid. I don't think that the existence of FFI in itself would have any effect on the 'argument' that one side or the other would make for recovery of prosecution/defence costs, but whether you would be able to recover the FFI (and I think that this is what you're asking) if found not guilty of an offence that was directly related to the intervention, I don't know.

If there was an investigation of a material breach which led to a prosecution all the costs up until approval of the case (or submission to COPFS in Scotland) would be recoverable through FFI. In the event of a not guilty verdict the costs recovered through FFI would have to be refunded. Costs relating to the running of the case itself would need to be resolved through the normal application to the court for costs (in E&W, costs aren't recoverable in Scotland).