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If you have some ability with HTML/CSS you could convert the LIT again with the Convert - Debug feature enabled (ignore the resulting MOBI).
If you examine the Debug directory (Input subdir is usually helpful) you can examine the html Calibre extracts from the LIT. This may point you at the problem. Sometimes you can then fix the problem by using the Convert - Look&Feel - ExtraCSS to override the problem formatting in the LIT when you convert to MOBI again.
Other times a manual fix of the Debug html is necessary. In which case you can then import the fixed html into Calibre as the new source file and discard the LIT.
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