An HTTP challenge will likely be 5 (unlikely but could be 4) HTTP requests to your server for the same URI. Do you know what those other files that show in that folder are?
The problem reported is that after the first HTTP request that worked the LE Server then got returned a mostly empty reply instead of the challenge data it expected.
What does your Apache access log look like for an actual cert HTTP challenge? How many do you see with the same URI and what were the HTTP response codes (all "200"?).
Interesting, if I try your test file multiple times there is some sort of caching affecting the replies. Note the second is a HIT. Could this be affecting the HTTP challenge somehow?
curl -i http://cube.blackrosetech.com/.well-known/acme-challenge/index.htm
HTTP/1.1 200 OK
Date: Mon, 16 Sep 2024 02:28:56 GMT
Server: Apache
Last-Modified: Mon, 16 Sep 2024 00:27:54 GMT
...
X-Cache: MISS from cube.blackrosetech.com
test
curl -i http://cube.blackrosetech.com/.well-known/acme-challenge/index.htm
HTTP/1.1 200 OK
Date: Mon, 16 Sep 2024 02:29:10 GMT
Server: Apache
Last-Modified: Mon, 16 Sep 2024 00:27:54 GMT
...
Age: 14
X-Cache: HIT from cube.blackrosetech.com
test