“With reference to …” is rather old-fashioned. I remember using the phrase years ago. Have you read it before? Do you use it? Such as in: “With reference to your letter …”.
My recommendation? Just say “thank you”. Something like: “Thank you for your letter”. Or “Thank you for contacting us.”
Instead of writing: “With reference to our meeting last week”, you could write: “It was a pleasure meeting you in Cologne last week”. Or even: “I very much enjoyed meeting you in Cologne last week”.
And instead of writing: “With reference to our conversation yesterday”, you could write: “I enjoyed talking to you yesterday”.
I find these phrases much more personal. Do you agree?