When typing markdown, in a #%% [markdown] block, only single line comments are considered as markdown.
Example input
#%% [markdown]
"""
# Lorem Ipsum
Lorem ipsum dolor sit amet, consectetur adipiscing elit.
Nullam eget varius ligula, eget fermentum mauris.
Cras ultrices, enim sit amet iaculis ornare, nisl nibh aliquet elit, sed ultrices velit ipsum dignissim nisl.
Nunc quis orci ante. Vivamus vel blandit velit.
Sed mattis dui diam, et blandit augue mattis vestibulum.
Suspendisse ornare interdum velit. Suspendisse potenti.
Morbi molestie lacinia sapien nec porttitor. Nam at vestibulum nisi.
"""
Output

Desired output
Commenting every line separately does the trick:
#%% [markdown]
# # Lorem Ipsum
# Lorem ipsum dolor sit amet, consectetur adipiscing elit.
# Nullam eget varius ligula, eget fermentum mauris.
# Cras ultrices, enim sit amet iaculis ornare, nisl nibh aliquet elit, sed ultrices velit ipsum dignissim nisl.
# Nunc quis orci ante. Vivamus vel blandit velit.
# Sed mattis dui diam, et blandit augue mattis vestibulum.
# Suspendisse ornare interdum velit. Suspendisse potenti.
# Morbi molestie lacinia sapien nec porttitor. Nam at vestibulum nisi.

When typing markdown, in a
#%% [markdown]block, only single line comments are considered as markdown.Example input
Output
Desired output
Commenting every line separately does the trick: