pathogen.vim versions after 1.2 (2010-01-17) have a pathogen#helptags function that will automatically update the help tags for each directory in the runtimepath. Just call it after you call pathogen#runtime_append_all_bundles:
call pathogen#runtime_append_all_bundles()
call pathogen#helptags()
Or, assuming you have call pathogen#runtime_append_all_bundles() in your .vimrc:
vim -c 'call pathogen#helptags()|q'
from the command line only once after you have fetched the updates.
Recent versions of pathogen recommend calling pathogen#infect() in your .vimrc instead of pathogen#runtime_append_all_bundles (since b147125 “Add pathogen#infect() as primary entry point for basic setup”, 2011-05-13; the former calls the latter internally). If your .vimrc is calling pathogen#infect(), then put your call to pathogen#helptags() after that.