.htaccess in subfolder work partially

Question

The website's structure is the next:

www.mydomain.com -> Here is installed wordpress.
www.mydomain.com/subfolder1 -> Here is installed a custom php Application. www.mydomain.com/subfolder1/subfolder2 -> Here is installed Control panel of php Application.

I have an .htaccess in subfolder1 and another in subfolder2, the navigation in subfolder1 is great, but the navigation in the subfolder2 is wrong;

I can see the www.mydomain.com/subfolder1/subfolder2/index.php but if i want navigate in the menu ie www.mydomain.com/subfolder1/subfolder2/test the url change, but i see always the index.php

Any advices?

.htaccess in subfolder1

Option -Indexes
ErroDocument 404/404.php
RewriteEngine On
RewriteBase /subfolder1/

#Remove extra trailing slashes
RewriteCond %{REQUEST_URI} ^(.*)/{2,}(.*)$
RewriteRule . %1/%2 [R=301,L]

#Add missing trailing slash
RewriteCond %{REQUEST_URI} /+[^\.]+$
RewriteRule ^(.+[^/])$ %{REQUEST_URI}/ [R=301,L]

RewriteRule /(uploads/.*) $1 [R=301,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l
RewriteRule ^(.+)$ index.php?url=$1 [QSA,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?$1 [L,QSA]

RewriteCond %{THE_REQUEST} ^[A-Z]{3,}\s(.*)/index\.php [NC]
RewriteRule ^ %1 [R=301,L] 

<ifModule mod_deflate.c>
<filesmatch "\.(js|css|html|jpg|png|gif|eot|woff|ttf|svg)$">
    SetOutputFilter DEFLATE
</filesmatch>
</ifModule>

<FilesMatch "\.(htaccess|htpasswd|ini|log|sh|inc|bak|cache|tpl)$">
  Order Allow,Deny
  Deny from all
</FilesMatch>

.htaccess in subfolder2 is similar subfolder1 but i have changed the RewriteBase

Option -Indexes
ErroDocument 404/404.php
RewriteEngine On
RewriteBase /subfolder1/subfolder2/

#Remove extra trailing slashes
RewriteCond %{REQUEST_URI} ^(.*)/{2,}(.*)$
RewriteRule . %1/%2 [R=301,L]

#Add missing trailing slash
RewriteCond %{REQUEST_URI} /+[^\.]+$
RewriteRule ^(.+[^/])$ %{REQUEST_URI}/ [R=301,L]

RewriteRule /(uploads/.*) $1 [R=301,L]

RewriteCond %{REQUEST_URI} ^/subfolder2(.+)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l

RewriteRule ^(.+)$ subfolder2/index.php?url=$1 [QSA,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l
RewriteRule ^(.+)$ index.php?url=$1 [QSA,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?$1 [L,QSA]

RewriteCond %{THE_REQUEST} ^[A-Z]{3,}\s(.*)/index\.php [NC]
RewriteRule ^ %1 [R=301,L] 

<ifModule mod_deflate.c>
<filesmatch "\.(js|css|html|jpg|png|gif|eot|woff|ttf|svg)$">
    SetOutputFilter DEFLATE
</filesmatch>
</ifModule>

<FilesMatch "\.(htaccess|htpasswd|ini|log|sh|inc|bak|cache|tpl)$">
  Order Allow,Deny
  Deny from all
</FilesMatch> 

Answer 1

You have changed the RewriteBase, so you don't need to put "subfolder2" in RewriteCondition and RewriteRule.

Or keep that and change the RewriteBase as the first .htaccess