Any chance you have a backup copy of the catalog and can start over using a copy of the backup?
This part has me worried:
"What id did do was an mix of synhronising folders, looking for lost folders, relinking individual files and probably a lot more which stress has made me forget."
It should be really simple to copy all the images from the external drive while maintaining the folder structure by doing a drag/drop in Finder, then from LR Library module, Folders pane, "relocate" the top-most folders.
Yes i found a back up from 7 days ago so i'll use that.
It's just now i don't want to make the same mistake so what is best practice in asking lightroom to now use drive B and not drive A as the source for the folders.
I was sure yesterday i tried to do this using 'update folder location' which got me into trouble/
As long as drive B has the same directory structure as drive A, things should to very smoothly.
First, do NOT do any imports nor synchronizing nor moving nor drag/drop nor merging.
What you need to do is "relocate" just to tell LR where the files and folders are now.
Start with the folders as this will solve 99% of the problems.
In the Library module, Folders panel, expand the folders by right-click "show parent" to see the full paths.
Using the top-most folders that exist on the new drive, right-click on each top-most folder and select "Update folder location".
Navigate to the new folder location on the new drive. Make sure you select the folder with the same name and not the parent folder.
Repeat as needed for each top-most folder.
After relocating your folders, take a look at your images in the grid view. Most (all?) should no longer be marked as missing.
For any that are still marked as missing, use the standard "find missing photo" procedure.