Foo[*]
[*]: https://en.wikipedia.org/wiki/Foo
Bar[*]
[*]: https://en.wikipedia.org/wiki/Bar
Current behavior: Both will link to https://en.wikipedia.org/wiki/Foo
Desired behavior: Latest instance of [*]: should supersede the previous.
Why: Personally, I often like to use reference-linking to keep the word from generating a big, distracting link when it may be a very minor thing only warranting a footnote.
However, it forces you to keep track of what footnotes have been used before, so you end up needing to use multiple asterisks or going down the list of traditional footnote symbols (i.e. *, †, ‡, §, ¶, #). Or, for number-styled footnotes, using either full-size numbers, ^sup^ syntax, HTML <sup>, or the unicode characters ¹ ² ³ ⁴ ⁵ ⁶ ⁷ ⁸ ⁹ ¹⁰ ….
No matter what approach you take, it's either inconvenient, not-aesthetically-pleasing, or a-little of-column-A-and-a-little-of-column-B. I'd much rather be able to define what an asterisk is linking to directly below the paragraph.
That said, even if you don't feel like having to keep track of what's been used before is a big deal, it does become one if you ever want to merge two notes that both use reference-linking together.
When merging two notes that both use reference-linking, you have to check for overlapping references and revise where necessary. This is relevant even if you don't use footnote-style references, since two notes might make the same term into a reference but point to different URLs.
I'm aware it's not standard Markdown behavior to be able to supersede previous references, but I also don't see any good reason (from an end-user standpoint) as to why it shouldn't be standard behavior for Joplin; since, it's not really a breaking change except in the edgiest of edge-cases where the note was erroneously providing multiple URLs to the same reference.