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Why do I not see any exe or apk files on my phone in the app?

If I use a file manager the files are there, but they are not listed in the UI of the app.

Is there a restriction somewhere I have enabled?

I download apk files and want to ftp them to my server at home, but not being able to see them, I can't.

Thanks.

APK files should be visible only from AndFTP default app folder (internal) or any "External" folder:
viewtopic.php?p=27245#p27245

I have a Pixel phone, so no "external storage".

What is the solution here please?

But do you see any "External" button to browse folder? Even if you don't have external storage.

Where would I see that please?

In your AndFTP configuration. See screenshot below