The slowdown is almost certainly due to the books now being a single large file. My PRS-300 is slow with big files so I split on chapters. (Calibre does this for me during conversion from a single large text file.)
You would probably be better posting in the Sigil forum since Sigil may also have the means of undoing what you've done. If that fails then you could resort to backups.
One last option may be to convert with calibre, but this seems a bit of a sledgehammer solution in this case.
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