Indeed, this is upsetting…
It makes me wonder about how exactly works this eyes thingy. Do the waking order of the eyes has to do with the number of crystals you've given to it, or with what crystal it is: in other words, with its origin.
In the first case, the third eye from the right is the last one for everyone, and if you don't remember from what scene the missing crystal is, I'm afraid you'll have to look for it everywhere again.
On the other hand, in the second case, it would be possible to link each eye to one crystal in the map. It will take some time but will be useful to help people in similar case! And perhaps this is even simpler: the sleeping eye location may show you the direction to take to find the missing crystal!
(that is not sure at all, but we'll have to test if there is something like this.)