Thank you for your question. Here is the ruling relevant to your case according to Ay. Sistani (hA):
Ruling 2354. If a safe keeper of a deposit is not negligent in safeguarding it nor excessive with it, i.e. he does not use it in an unpermitted manner, but it so happens that it perishes, he is not responsible for it. However, if he is negligent in safeguarding it - for example, he keeps it in a place that is not secure from being found and taken by an unjust person - or he is excessive - for example, he wears the clothing or rides the horse [that he was entrusted with] - then, in the event that it perishes, he must replace it for the owner.
Islamic Laws, annotated and translated by Mohammad Ali Ismail, volume 2, page 99-100
If your placing the amanat in your check in bag was not considered as negligent, you do not have to pay if the goods are damaged/stolen.
May you always be successful