Hi there so as discussed the employer must pay you the entitlement stated in your contract. If the clause does not allow the employer to use their discretion as to when to pay you sick pay and also the entitlement is not conditional on anything else, as long as you are off sick in general and for any reason, they must pay you.
If they do not pay you what you are due then it potentially amounts to an unlawful deduction from wages, which is made illegal under the Employment Rights Act 1996. It is also a breach of contract.
In order to try and resolve this, you should consider raising a formal grievance first. Next, the employer should be contacted in writing, advised that this is being treated as unlawful deduction of wages and ask them to pay back the money within 7 days. Advise them that if they fail to pay the money that is owed, legal proceedings could follow.
If the employer does not return the money as requested, the following options are available:
1. Employment Tribunal - the time limit to claim is only 3 months from the date the deductions were made. To make the claim, form ET1 needs to be completed and submitted - you can find it here: https://www.employmenttribunals.service.gov.uk/employment-tribunals
2. County Court – this is an alternative way to claim and the advantage is that the time limit is a much longer 6 years and is usually used if you are out of time to claim in the Tribunal. The claim can be made online by going to: www.moneyclaim.gov.uk.
Hopefully by warning the employer you are aware of your rights and are not going to hesitate taking further action they will be prompted to reconsider their position and work towards resolving this.