This sounds similar to existing Thunderbird bugs:
Inline spell checking randomly fails
[ . . . ]
The actions that cause the inline spelling to fail (i.e., the red
underlining to disappear) are normal editing. For example in one instance, I
noticed that backspacing over a word caused the red underlining to disappear
from a previous spelling error (a couple lines removed)).
Bugzilla-933813
What I found is that any new message checks the spelling correctly as you
type (underlines). Reply to any message and the check spelling as you type
does not work (no underlines). Setting mail.compose.max_recycled_windows to 0
works with both new messages and when you reply. I only have the english
dictionary installed.
Launchpad-Bug-1229172
I can't reproduce with TB18, html or plain text compose, and the mozillazine
steps
Open a new email message.
Type 'In the middle of the day'
Backspace until you only have 'In the mi'
Then retype the rest so you end up with 'In the middle of the day' again.
However, some say it is intermittent
Bugzilla-790475
Even if it's not the same bug, you can sometimes get ideas from other bug reports.
Dealing with intermittent or un-reproducible bugs can be frustrating.
I've been there many a time, and it's not fun.
Here's some things you could try:
Record a screen-cast of the bug when it occurs.
Try to avoid including any personal or identifying details.
This makes it a lot easier to show what's going on;
you can right-click and show you have "Check Spelling" enabled,
as well as what dictionaries are installed.
Does manual spell checking with Ctrl-Shift-P work?
Based on your comments, it sounds like it is,
and just the highlighting is broken.
This is something you could demonstrate in the screen-cast.
Is it reproducible for a particular message?
That is, can you hit reply, observe the bug,
then close and re-open Thunderbird,
hit reply on the same message,
and get the same bug again?
If you cut and re-paste the text,
does the spellchecking start working again?
In some bug reports, it seems like this makes a difference.
Does HTML or text composition matter?
If you hold down shift before clicking the "Reply" button,
it will toggle between HTML and text composition.
Try setting mail.compose.max_recycled_windows to 0.
It seems like it helped in other bug reports.
If you run Thunderbird from the console,
do you see any relevant error messages in the output?
This is a bit of a long shot,
but it might be worth a try.
Do you still observe the behavior if you run in safe mode,
i.e. Help -> "Restart with Addons Disabled"?
I'm guessing yes, but it's a good idea to test this
since it helps establish it's an issue with the core Thunderbird code,
not some ancillary extension.
Do you still observe the behavior if you make a new profile?
This can be time-consuming, but it's a very useful data point:
it means that it's not a quirk of your profile or settings.
You can also take a peek at the source code.
Sometimes just reading the comments can be helpful.
Here's some relevant parts for Debian buster:
Link-1, link-2, link-3
If you think it's worth submitting a bug, you can do so either via email with Debian or directly to Thunderbird here.