I have created a mod_rewrite that redirects from a particular URL to url.php and this is working properly. In this case I'm using a non-existing folder called store which means that when I try to access my application through:
/myapp/store/whatever
this will redirect me to:
/myapp/url.php

RewriteEngine on
RewriteRule ^store/([^/\.]+)/?$ url.php?store=$1 [L]

However, if I try to use the same rule on an existing folder it gives me a 404-page. So if I go to:
/myapp/whatever
I should still be redirected to /myapp/url.php

RewriteEngine on
RewriteRule ^myapp/([^/\.]+)/?$ url.php?store=$1 [L]

Can you please help me with this second rule?

I'm not sure if I follow your question. So I will lay out some details as I perceive them:

At www.example.com/myapp/ the folder /myapp/ is a physical folder on disk.
At www.example.com/myapp/store/ the folder /store/ is a virtual folder.

And "whatever" is a placeholder standing in for any represented content.

Your rule works on /virtual/whatever, but fails on /actual/whatever.

I run a wiki. I was advised in the setup instructions for generating a user-friendly URL scheme at www.example.com/wiki/, not to create an actual /wiki/ folder on the disk.

That may be what you ran into when you tried to work from the actual myapps folder.

Edit: Some additional thoughts come to mind: Your rewrite rule doesn't kick in when you are following an actual folder, and the "whatever" does not exist in the actual folder. Therefore, 404.

You may need to place some conditionals and a rewrite rule to capture "whatever" that is not in /store/"whatever."