I presume that your clerk is serving a period of notice as set out in her contract. Are the issues with her conduct and financial irregularities a recent development, or is this something that has been ignored for a period of time? You say that you have been advised to have an investigation meeting with her. Who gave you this advice? If she proceeds with an employment tribunal case against you, the normal way to address this would be to hand matters over to the legal team associated with your insurance company. Regardless of whether this happens, you should notify your insurance company immediately that there is a possibility of legal action against the council, as this is a condition of your insurance. You should also take advice from your internal auditor regarding Box 8 on the Annual Governance Statement on your AGAR.
Whilst you may ask the clerk to attend this meeting, you cannot force her to and it is unlikely that she will, particularly if she is receiving professional advice. You have already conducted an exit interview with her. This meeting will help you to build your case against the clerk and will not help her in any way. The standard contract of employment for a clerk requires one month's notice, so she would be advised to take sick leave to avoid meetings of this nature. Your disciplinary policy applies only during her period of employment. If the financial irregularities are of a serious nature and amount to fraud or theft, you should consider involving the police, but proof will be required in order for them to take action.
Finally, to address your question regarding the procedure for setting up the meeting, the answer may lie in your own policies and procedures, particularly the terms of reference of your staffing committee, if you have one, or whatever other arrangements you may have for line management or supervision of the clerk.