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No idea. What do you mean by "cleaning" messages? From what? The best and fastest way to split a single large file into separate pieces is to use regular expressions to insert Sigil split markers into the file and then split it all at once.
Alternatively, going to the end of the file and manually splitting each chapter off the very end results in the least number of file rewrites.
No changes to file splitting have been made recently at all so if something changed, it is because of changes on your machine, not Sigil. Perhaps some virus checker or system function is playing with Sigil's temp files? If so, you should set your own temp file directory via Sigil preferences or temporarily disable scanning of temp files by your virus checker.
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