Invalid URL Aliases in Drupal Nested Sites/Subsites - Main 404 I'm sure my title made no sense! But I'm really struggling with something and could use some assistance.

I inherited a Drupal-based website a few months ago, and it was my first exposure to Drupal.

The way this website is set up is that it actually has three separate Drupal installs. Clean URLs is enabled with aliases set up. I'm sure this was the complete wrong way to set up multi-site, but unfortunately it is this way for now and I'm not confident I could correct it without breaking many things.

www.website.com (1st Drupal Install)

www.website.com/success (2nd Drupal Install)

www.website.com/spa (3rd Drupal Install)

For awhile, everything was working fine. But at some point the URL www.website.com/success/thank_you, started to display a 404 error - but NOT /Success's 404 page - it would be the 404 display page of the base Drupal install! But still show www.website.com/success/thank_you in the URL

Other Aliases on /Success continued to work, etc www.website.com/success/online, www.website.com/success/privacy.

If I typed in a garbage URL, say, www.website.com/success/abcdefg, i would get the 404 page of /Success install like it should, not the base Drupal.

I managed to "fix" this issue by changing the URL Alias of /success/thank_you to /thankyou.

Now last week, it started happening with the other Aliases.

If I go to /success/thankyou it still works properly. If I do /success/online, or /success/privacy, I get the main Drupal's 404 page.

If I remove the Alias, I can do /success/node/20 and see the page. If I change the Alias to say, /success/online2 I can see the page. But if I change it back to /success/online, it does not work.

So, my current thinking has been that this is an issue with the base Drupal install, not the /success Drupal. That the base Drupal is grabbing that URL I am entering for some reason and seeing it's not an alias in that Drupal and failing. But why is it only happening to specific aliases? And why doesn't the base Drupal grab the URL if I type in a garbage one? (/success/abcdefg for example).

Any pointers in the right direction would be greatly appreciated.
Option 1 - base_url
Maybe you want to do some experiments to see if setting the $base_url in your settings.php somehow helps.
Option 2 - RewriteRule
It might be worth trying to further enhance your .htaccess file, by adding a line after the line containing RewriteBase, which looks like so:
RewriteRule . index.php [L]

For more details on the above line, refer to the (accepted) answer in this question on StackOverflow.