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£2000 loan - You have something in writing but does it also give payment terms (4 payments and when each payment is due), or was that a verbal agreement? Secondly did the owner state they would pay or the business would pay, as its key to get the owner to by liable no the business (if its in difficulty).
Missing payslips - Yes your employer is responsible for providing pay slips, you should be able to ask your employers accountant normally as they run the payroll for them, but it may be the employer is doing it themself to save money.
Transfer of funds - Its not technically illegal but it becomes very complicated when proving where money is going, for instance if HMRC audited the business bank it wouldnt be unreasonable to assume those payments went to you, and potentially would cause a fair bit of grief for you to prove you not liable for income tax.
Knowingly paying someone who is not paying tax would make you complicit, however if you report the matter to HMRC and explain that you were not 100% sure but certainly under the impression this may be the case and ask them to investigate would show a willing to put things right, would put you in good light. However it may be possible the staff were contractors and working as sole traders, but that is unlikely.
A director, manage, cleaner the role you have doesnt really matter.
If the task give by your manager (eg business owner) then you were following the ask of the business.
The only difference comes in when it comes into filing tax returns or signing for things on the companies behalf.
Yes complicit as an employee following instructions of the business.
If you are confident that tax evasion is occurring report your suspicion to HMRC, thats is all you need do to show a reasonable effort to flag up unlawful behaviour.
I havent heard from you in some time do you require any further assistance, or are you happy for me to mark the question as resolved?