If you want to avoid the problem of choosing to use the second or third person singular possessive form, you could just write,
'in appreciation of an enjoyable and enlightening seminar.'
But in answer to your question, if the certificate addresses Mr A in the third person - ' is presented to Mr A', then you need to be consistent and use 'his' not 'your'. It sounds a bit messy and confusing to use 'your' in this context.
Student or Learner