If you own the house, and placed an item into a locked down or secured container, then you should be secure in knowing that the item will always be there later on. 100% sure that this is the case with all items, placed in locked down or secured containers.
If there was a rolling restart it would have had to roll back to a time prior to the nice person giving you the two pets in question.
As for unlocking an item in a locked down container, and not locking them down again, this is a possibility. But you said you did not touch them so that should not be the case, here.
Since you are new... items that are not locked down, or secured, decay after 2 hours in the game world. A pets happiness decays over time as well, but I believe this is put on pause if you shrink the pets down. (only 90% sure on that one)
Other then that, I don't think it was in your control, nor do I believe it can be reversed, or replaced. However, I believe there are plenty of players willing to help you get new pets when you are ready, and able, to use them.
Let me know when that time comes.
(my taming is GM, but I can always get it to 120+ should I need to)
--Sturger--