I can't see what your problem has to do with Matomo. Matomo requires it's index.php, so you can't simply overwrite it with another file.

Hi, Matomo overwrite it self the index.php, I was to have to restaure the index.php from official Matomo zip.

It's Matomo features, see: #10414

Now it's clear what you meant, but that shouldn't happen for the root directory of Matomo. Are you able to reproduce that?

But it happen for the root directory of Matomo. I have not test again, but it's have happen few time I have edited the bootstraps to disable the "eaccelerator disabling function". But maybe unlinked