TeX Live installation is missing tlmgr, how to fix?

It should be safe to install TL again with the same location settings, and this time only select tlmgr. (I'm surprised tlmgr is not part of the 'essential binaries' group anyway.) I think it would be safe to uncheck all "macros for XXX" options sice they will not be erased from a previous install, I'm less sure about font options.

Are you installing a version of TL provided by Debian/Ubuntu? Those have been known to remove tlmgr in the first place, since it's a packaging mechanism that bypasses the distribution's own.)