Is there any reason to keep this folder and its contents?
I'm thinking if I go back to tweak something, its going to generate a whole new set of jpgs.
Keeping the intermediary sequences normally makes a lot of sense, if you eventually want to redo the video only - for example - different resolution, different framerate, different motion blur setting.
If you reedit the sequence itself, of course you will have to reexport from Lightroom, in that case the LRTExport Plugin will normally overwrite the old intermediary sequence.
My recommendation would be to use a dedicated harddrive (harddrives are cheap these days) and keep the intermediary sequences. I find them very valuable for my work. But of course - you can always redo them - but it takes time.
I have been copying the folders to external drives... Should I "remove" the folders from LR... or does the size of the LR catalog effect performance at all? It seems my export function is getting slower and slower...
Normally the amount of images in the LR catalog does not have any significant influence on the performance.