New MSI?  Did you build it yourself?  If you have, what I recommend is
updating the "version" of the software; and set the new MSI to upgrade the
previous version.  If you have absolutely no clue what I'm talking about,
there is a course from desktopengineering.com that can help you demystify
Windows Installer for the SMS/ConfigMgr admin.

Otherwise, what I would do if you can't set the MSI to be a new version &
guid; I'd probably chain two things together:  an uninstall of the previous
version, then an install of this new .MSI.  I wouldn't replace the existing
.MSI on your DPs yet--your clients may need to reference the old one on the
DPs in order to successfully uninstall.

Just curious: what's the MSI for?  Unless this is a home-grown application;
most vendor apps already come in MSI format.  You as an admin should really
only ever create Transforms (MSTs) to customize their install to fit your
environment.