At the end of a run, tlmgr takes a number of actions, in the following order:
- run
mktexlsr;
- run
mtxrun --generate which is the equivalent for ConTeXt, if it is installed;
- run
updmap-sys with the proper arguments if necessary (roughly, if font packages got installed/removed);
- regenerate language files (
language.dat etc) and run fmtutil-sys with the proper arguments if necessary;
So, if mktexlsr failed and you had to interrupt tlmgr, the following actions have not been taken. Now, if you don't use ConTeXt and the packages updated didn't require a run of updmap-sys nor fmtutil-sys then running mktexlsr (with sufficient permissions) is enough.
If you want to be sure, you can check in TEXMFSYSVAR/web2c/tlmgr.log (where the proper value of TEXMFSYSVAR is given by kpsewhich --var-value TEXMFSYSVAR, usually /usr/loca/texlive/2011/texmf-var) the list of recent actions taken by tlmgr, eg:
[Sun Jul 24 12:49:17 2011] update: xdvi.x86_64-linux (22625 -> 22971)
[Sun Jul 24 12:49:18 2011] update: xdvi (22089 -> 23138)
[Sun Jul 24 12:49:39 2011] update: xetex.x86_64-linux (22625 -> 23143)
Then, to be absolutely sure everything's ok, you can reinstall these packages using
tlmgr install --reinstall xdvi.x86_64-linux xdvi xetex.x86_64-linux
(assuming the previous example was the complete list of updated packages).
tlmgr update --all --selfso thattlmgrupdates itself if required. Otherwise it will stop with an error if it need to be updated itself. – Martin Scharrer♦ Dec 22 '11 at 11:04