The 21-year-old had faced charges of trying to groom the youngster on social media sites more than three years ago.
However, the charges were shelved by prosecutors due to lack of evidence.
A source said the family of the girl – now aged 16 – felt “let down”.
The latest twist comes a year after Thomson was put on the sex offenders’ list after he admitted vile online chats with two youngsters aged 12 and 14.
Both Hearts and the ex-Scottish under-21 star – who is on loan at FK Suduva in Lithuania – were unavailable for comment.