All collections gone - everything is now in "without keywords"

Just to clarify, are you maybe using Lightroom (cloud) as well as Lightroom Classic (local files) - or only LrC?

These are two distinct systems which work in different ways and have different features - not two aspects of the same system - hence any reorganisation or keywording done in one, is not going to transfer 100% the same into the other.

all collections are have folders and subfolders

Do you actually mean that you created Collection Set(s) and placed individual collections within the collection set?

and noticed all my collections were gone.

Is the collections panel hidden perhaps? Over on the left, point mouse over any panel heading, right click, and turn visibility of collections back on.

I have been sorting my Lightroom Libery into a system that works great for my workflow

Please describe this in a lot more detail, step by step. Is one of the steps to import the photos again?