In a similar situation to you I make Firefox my default browser and it includes timimi so I can save wikis with a file address.
This allows me to build a directory of links inside a tiddlydesktop wiki that will open them in the browser. Tiddly desktop allows my directory wiki to open file explorer on a particular folder and applications and more.
I have not come across your problem and will look when back at my desktop. I am s upprised.
Perhaps look at the way you have built your links, have you tried the html a and href method? Even to your tiddlydesktop wikis.
I think tiddly desktop needs some command line options to open a wiki in tiddlydesktop.
Regards
Tony
https://tiddlywiki.com/#Filter%20Operators
[[Filter Operators|https://tiddlywiki.com/#Filter%20Operators]]