Hopefully nothing will come of it but if this was a C2W bike then, irrespective of the involvement of Cyclescheme, the transfer to the employee must be at market value. If it was not you have received a benefit in kind to the extent of the gap between your payment and the actual market value. You are taxable on that benefit. If HMRC call for the money it is your problem.
And in making that point I'm not trying to be combative or 'clever'; just pointing out the facts as they are on the ground.
In practice, that will not happen and I will tell you why. You have relied on your employer to administrate the scheme efficiently and within the rules. The fact they have failed to charge you the market value of the bike is a failure on their part. HM Revenue and Customs will pursue the employer for their failure to complete form P11d properly (for which there is a wacking penalty of £3,500 per employee or something) and the employer will negotiate a settlement with the Revenue to save any further enquiries into their PAYE matters. In the event that the Inland Robbery pursue you for any aspect of the transaction all you need do is say you relied on your employer to issue form P11d with the correct amount of benefit (ie the difference between the sale value and the market value) and as this was not on your form P11d, you did not benefit. It's a technicality, but by virtue of having no form P11d or no entry on form P11d you should be able to escape tax. That's my view anyhow. I have never seen an employee being pursued for a non existent entry on a P11d i.e. an unrecorded benefit. Since by definition if it is unrecorded it is a failure on the part of the employer not the employee.
The end result is employers pulling out of Cyclescheme arrangements or starting to charge market value, since the cost of default (investigation, penalty, interest, professional advice) is much higher.*
*Or as someone has intimated they can include the benefit on form P11d, you pay the tax (usually via your tax code or tax return filing), they pay Class 1a National Insurance and everyone escapes censure.