[BUG] File doesn't encode properly, video cuts off before it's finished

[Selur]

And if you have progressive content that you do NOT want deinterlaced? What do you do? You avoided that question entirely.

Deinterlacing&Co only applied if the source is not progressive.
So the setting under 'Auto deinterlace handling' is not used if your source is progressive.
What is unclear about the tool-tip of that function to you?

Deinterlace handling:
Sets what method will be used to deal with non-progressive content, assuming the output isn't marked as interlaced in the encoder.
Hybrid does only deinterlace if:
a. the source is non-progressive
b. the output is not interlaced
So:
- If your source is flagged as interlaced, but in reality is progressive: overwrite the scan type.
- If your source is flagged progressive, but in reality interlaced: overwrite the scan type.
- If your source is progressive and properly flagged, do not worry Hybrid will not try to deinterlace the source.

You entirely upended a crucial function of the software with no explanation why or how it's supposed to work going forward.

No, clue what makes that selection to the 'Auto deinterlace handling' crucial in your eyes.

You're a software developer who uploaded their work publicly, presumably you're developing software for people to use, not just for personal use.

Now that you mention it, https://www.selur.de/licence clearly states:
Hybrid itself is free for personal usage without a hassle.

Hybrid is provided "as is", without any guarantee made as to its suitability or fitness for any particular use. It may contain bugs, so the use of this tool is at your own risk. The author takes no responsibility for any damage that may unintentionally be caused through its use. You may not distribute Hybrid in any form without written permission of the author.

So far no one's commented positively on the change but it's caused a lot of confusion and negativity.

Seems, to me, like that change only caused 'a lot of confusion and negativity' to you.

"If you don't like the massively upended UI that no one has reported positively on, do not use it" is a weird flex.

'massively upended UI ' counting the removal of a single option in a drop-down menu massive seem like an overstatement.
So you expect me to change the UI however a single 'confused and aggressive' user wants it to change?
Suggesting such a user, to use another software seems to be the sensible way. (I may be wrong there.)

Cu Selur

Ps.: Just a thought, maybe hiding the whole Deinterlacing setting whenever a source that isn't marked as interlaced is loading could help confused users.