I would check with the staff of Library and Archives Canada to make them aware of the irregularity, but also talk to the staff of the Royal Regiment of Canadian Artillery Museum - I think they may have duplicate copies of unit war diaries. Unfortunately, they also charge researching fees but I wonder if they wouldn't waive that in order to do an integrity check on their files.
Of course, if you obtained the copy of the war diary from them in the first place rather than LAC than the above doesn't help.