Running quarto render on a doc with an embed shortcode under a different profile/metadata settings requires manual deletion of the .quarto/embed directory between renders

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

I think I have come across a little edge case.

I am rendering a document which uses the embed shortcode, however each render is under a different Quarto profile, e.g.

quarto render --profile combined-questions
quarto render --profile combined-solutions

One of the differences is that under one profile I have

execute:
  eval: false

and under the other

execute:
  eval: true

Quarto fails to detect this difference and hence doesn't rerun the embedded qmd files on the second render.

At first I thought this was related to caching or freezing but I find that none of those options make a difference. So I went digging in the .quarto directory. I find that manually deleting the ipynb files in .quarto/embed gives me the rendering results I expect (as then they are regenerated during the second render).

rm -rf .quarto/embed
quarto render --profile combined-questions
rm -rf .quarto/embed
quarto render --profile combined-solutions

My example repo is https://github.com/remlapmot/tutorial-quarto-profiles.

The correct combined-solutions output document is: https://remlapmot.github.io/tutorial-quarto-profiles/tutorial-combined-solutions.html
whereas the incorrect one is https://remlapmot.github.io/tutorial-quarto-profiles/tutorial-combined-solutions-incorrect.html (it's the three code chunks for Python, Stata, Julia which should have output at the bottom which are wrong/were not re-executed).

So I think you need to store the profile/metadata arguments along with the embedded ipynb files and check if those change, and if so automatically regenerate the ipynb files in .quarto/embed.

I'm on Quarto 1.7.32.

Steps to reproduce

Example in linked repo.

Actual behavior

quarto render doesn't apply the different profile/metadata settings to the generated ipynb files for embedding in the second render.

Expected behavior

quarto render should apply the different profile/metadata settings to the generated ipynb files for embedding in the second render.

Your environment

• macOS 15.5

Quarto check output

% quarto check
Quarto 1.7.32
[✓] Checking environment information...
      Quarto cache location: /Users/tom/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.85.1: OK
      Deno version 1.46.3: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.32
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/tom/Library/TinyTeX/bin/universal-darwin
      Version: 2025

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
      Source: MacOS known location

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.13.5
      Path: /Users/tom/Documents/GitHub/tutorial-quarto-profiles/.venv/bin/python3
      Jupyter: 5.8.1
      Kernels: python3, nbstata, ark

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.5.1
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
      knitr: 1.50
      rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

Simpler reprex

I made a simpler example with just R and Python

uv sync
source .venv/bin/activate

# Example with just R and Python

## correct second render
rm -rf .quarto/embed
quarto render --profile combined2-questions
rm -rf .quarto/embed
quarto render --profile combined2-solutions

## incorrect second render
rm -rf .quarto/embed
quarto render --profile combined2-questions
quarto render --profile combined2-solutions