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This isn't a very technical answer - but I've never had an issue clearing them.
I don't know where they're used, exactly (if at all), but there are many cases where one of the suggested steps in troubleshooting an issue is to delete/rename the bookmarks.nsf - so they're obviously rebuilt if needed.
I'd say go for it.
Feedback response number WEBBB2LJP7 created by Mark Taylor on 07/12/2018