My experience over the years is that it's rarely, if ever, possible to install a Fixpack over a hotfix.

The hotfix must be removed first, then the next Fixpack can be installed.

I wanted to try this (removing a hotfix) on a test server which has the same issue. The version there is 901FP7HF370 but there isn't such a filename at fixcentral.

How can I remove this hotfix? 

The first time it installs the hotfix, the second time it will uninstall it.

HF240 appears to be IF3 (I assume you're running Linux)?

http://www-01.ibm.com/support/docview.wss?uid=swg21657963

I don't find FP7HF370 listed here...

For that very reason, whenever I update a server, I keep a copy of the current install files on the server - so that I can remove the current FP or HF when installing new.

The only other way I know of would be to remove Domino, then reinstall 9.0.1, then the current FP and HF. 

Oh, you could open a PMR to get the code if you can't find it anywhere!

Thank you Mark! It seems that IF3 for FP7 cannot be downloaded. And the link for IF3 on the support page points to IF4 in Fixcentral.

The procedure I follow is this: Run the base install of 9.0.1. This gets the installation back to 9.0.1. Apply the current Feature Pack and then any Interim Fix. If a hotfix has been provided to us by IBM, I would then apply the hotfix on top of the Interim Fix.