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@DNSB is correct. There's not "two different" forms of hex codes being used.
As far as manually creating these files ... more power to you, but that wasn't really taken into consideration when the Saved Searches feature was first implemented. The actual creation of the file is handled by Qt in such a way that the same code will work in cross-platform situations. But since Qt automatically handles things like line endings, it's not likely that a file created on one platform will always be 100% compatible with Sigil on another platform.
I will look to see how Qt creates the file, though. Perhaps something in python could be done to change unicode into the hex representation that Sigil expects the file to be in.
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