Well, I'm trying also to understand the problem

Although this is not directly related with your question, it looks to me that is the same problem as to find an unique name to each seedling of each seed tray in a greenhouse, all cells must be different, so you have a matrix for each plate, and them you need a parent hash covering all matrixes.

You could have either a "parent" hash with samples=Keys and cells=values or either want a hash when plate cells will be keys and values = sample tags. I think the former is better cause you can't repeat a sample tag, but you can have four cells named B5 in different trays

So if I'm not wrong this is a problem related with

1- to assign tags according some rules to each key/element of a hash of hashes. Something like to identify the sample_BXC35 (key) with its hash value "i'm-the-cell-AF23-in-the-fourth-small-sized-plate"

2 - to print a tridimensional hash, a hash of hashes covering all your "seed-trays"

I suggest to read about tridimensional hashes and maybe also you will find useful to read about the Data::Dumper module