This happened to us at the end of last school year.
I complained that the home-school contact book was being used as a threat (as in - "ds1 this work should be easy for you, if you don't do it better I will write in your contact book that you have been naughty and then your Mum and Dad will be cross with you" from his maths teaher 
) and also as a means of telling tales on ds for minor things that other children's parents would never be aware of (eg "ds1 spoke to his friend after the whistle had gone at playtime"). This was plainly wrong, as they whole point of the book, as agreed with the Head and SENCO was so we could keep in touch regarding the bullying that ds was experiencing and try to improve his hatred of school in general.
Anyway, the final straw came when ds's class had a supply teacher - yet again - and their ICT lesson was cancelled at the last minute in favour of singing practice. Obviously this was dire for ds. They had a change of teacher for the third time that day, it was his beloved ICT that was cancelled, they didn't tell him in advance that the timetable had changed and it had already been cancelled twice that month. So, ds got really upset, disraught in fact. The supply (who is internal cover and knows ds) told him he was very bad and being naughty, making a fuss about nothing. He became hysterical, sobbing and crying etc, so another teacher (the singing teacher) came in and started shouting at him as well. She, in her wisdowm, told him he was extremely naughty and if he didn't start behaving she would set him extra work and he could do it in her classroom instead of singing and during play and lunch the next day. All this was written in the contact book as if ds had been very naughty for no justifiable reason.
I was furious and ready to make a formal complaint, but low and behold, his contact book (thus my evidence) went missing the very next day. 
His teacher reckoned it disappeared off her desk. Now that meant, either she was trying to pull one over on me - or it had been taken off her desk by one of the other children who had a contact book (one of whom was ds's main bully!). She swore they'd turned the classroom upside down looking for it, but had no luck. I wrote a letter outlining my concerns about a book containing details of bullying incidents and other sensitive information etc going missing, possibly taken by the bully etc.
Then suddenly on the last day of term, she came out at the end of the day claiming she'd found it under some paperwork in the store room.
I think she kept it until it was too late for me to complain 'on her watch' then gave it back when he was leaving that day, so if I'd tried to do anything about it at that point I would have just looked petty.
Anyway, I'm ranting - am still very angry about the whole thing as you can probably tell - but my point is, that some schools are not above this sort of devious behaviour in an attempt to wrong-foot or undermine you.
My advice would be to not let them get away with it and push for them to give you the supposedly coffee stained book.
Incidentally, I refused to let him have a contact book this year. Instead I created my own 'feelings diary' for him to fill in with the teacher regarding how he felt throughout the school day. I cited 'misuse/misunderstanding of the purpose of the contact book last year' and 'a need to help ds identify and manage his emotions with regard to school and learn to understand that he feels a range of emotions throughout the week rather than just sadness/anger/fear' as my reasons. It went really well at first, but they have only filled it in once in a fortnight now. [head banging emoticon]