Alex Riesen wrote:

Do some of your branches miss the commit by which it was removed?

git-clone followed by git-checkout master recreates the problem.

But to answer your question directly, I rebase, so they absolutely do 
not miss any commits.

It is somewhat unclear what "reappear" means, though: do you mean

Attempts to give you precise output to answer your question yielded a 
data point, the kernel's "make distclean" causes this:

[jgarzik@pretzel linux-2.6]$ make distclean && git checkout master && 
git diff HEAD
D       include/asm-blackfin/macros.h
Switched to branch "master"

diff --git a/include/asm-blackfin/macros.h b/include/asm-blackfin/macros.h
deleted file mode 100644
index e69de29..0000000

[jgarzik@pretzel linux-2.6]$ git checkout -f

[jgarzik@pretzel linux-2.6]$ make distclean && git checkout master && 
git diff HEAD
D       include/asm-blackfin/macros.h
Switched to branch "master"

diff --git a/include/asm-blackfin/macros.h b/include/asm-blackfin/macros.h
deleted file mode 100644
index e69de29..0000000

[jgarzik@pretzel linux-2.6]$ git checkout -f

[jgarzik@pretzel linux-2.6]$ git checkout master && git diff 
HEADSwitched to branch "master"

[jgarzik@pretzel linux-2.6]$ git checkout master && git diff HEAD
Switched to branch "master"

[jgarzik@pretzel linux-2.6]$


So, not a git problem but a kernel Makefile problem.  Sorry for the git 
noise.

	Jeff