Yes, I’ve brought this up before, but AmberV has suggested it warrants its own Bug report.
The command Document | Convert Formatting to Default Text Style removes any links from the document converted. Easy enough to verify by creating an external link or Scrivener link and running the command.
Convert Formatting was devised to facilitate a common document format: typeface, size, indentations and spacing. But it was meant to leave text formatting alone: bold, italic, colors, etc. Links involve text formatting and content, and this command should not tamper with them.
Best workaround for now is set a document format with the Format Bar. This will retain text formatting, including the links, but requires you to set the document format values manually rather than apply a default.
Thanks for taking a look – Jerome