I have this problem when using the WYSIWYG editor.
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Add a new link using the GUI, e.g.
https://github.com/eight04/jn-npp-emmet
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The link has seemingly been added correctly.
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Switch to a different note and then back (or switch to Markdown mode and back)
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The link has been converted to text.
This seems to affect all links that have same "URL" and "Text to display". If the two are different, then those links seem to survive.
Is this how the WYSIWYG editor is supposed to work? If yes, is there any workaround? I usually prefer to keep my links displayed as the actual URL. The main problem here is that the right-click menu to open them is absent when they become just text .
Tested in Joplin v2.3.5 under Windows 10.