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Usually the little drop down box only shows the expressions you wrote there last - if you write the expression checking things out in the regex builder, the expression you type on regex builder will not show up on the drop down menu. I work around it doing copy and paste.
About 3 expressions not being enough to clean everything out, if you are cleaning leaving the replace field empty (just deleting), you can on the same regex field use OR to use several different regex expressions. For example
(example1|example2|example3) - it can get pretty long
if itīs around a page break < hr > tag use OR at will before or after, or try to make the regex more general. But you can aggroup different expressions with OR and it will match any of them - though keep in mind it will try to match each one in order, left to right, it can be useful to put the narrowest first, and the more general last (sorry if this makes no sense, I am no good at explaining this in english).
About converting a converted mobi, well when you click convert again, it will give you a choice between if you want to convert from pdf or mobi. If pdf then of course the first changes are discarted, if mobi, well, itīs already different code, the logical expression which would match the pdf-to-html might not match the mobi.
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