Well, let's say I've done that in the past myself and it wasn't such a huge deal after all.
Here is what happened in my case:
Few years ago, when I was wearing Invisalign, the bottom tray fell in the bathroom and it was impossible to retrieve it again. I had the upper arch tray still on, but lost the lower arch tray.
I could have gotten my orthodontist to get me the 'copy' from the manufacturer, but I don't live in the US and thought it would take more time for that to arrive than me to go to the next aligner number (they're usually worn for 2 weeks).
So I just took the previous aligner (which I changed few days ago), placed it on my lower arch and that was it. I lost my no.6 tray, so I got the no.5 back on and waited for few days to get to no.7 on both arches.
Since it wasn't long till I could wear the next one (even 2 weeks is not that much to 'mess' up the treatment), the bottom Invisalign aligner fit OK. It was a bit harder to fit than the upper one, but nothing serious anyway.
My advice would be to wear the previous aligner (do not throw them when changing to the next number) and then replace with the correct ones, when needed. BE CAREFUL though with your aligners and try not to have this happen too often anyway.
Sure, a chat with your orthodontist is always good. Call your doctor when anything like this happens and see what he/she has to say about it. Maybe they can offer another solution, but this worked for me.