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The preferred method for maintaining tags in calibre is to use the tag mapper. Once you setup the rules for it, they will be applied automatically when adding new books/downloading metadata etc. this works much better in the long term than manually fixing tags, which should be a last resort.
Preferences->adding books->adding actions->rules to filter tags
Preferences->toolbars->Add the Tag mapper tool to one of your toolbars.
Preferences->Metadata download->Create rules to filter/transform tags
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