How to reproduce:

* mkdir /tmp/repos && cd /tmp/repos

* Create a .gclient file with:
"""
solutions = [
  { "name"        : "buildbot",
    "url"         : "https://skia.googlesource.com/buildbot.git",
    "deps_file"   : "DEPS",
    "managed"     : True,
    "custom_deps" : {
    },
    "safesync_url": "",
  },

  { "name"        : "pdfium",                                                   
    "url"         : "https://pdfium.googlesource.com/pdfium.git",               
    "deps_file"   : "DEPS",                                                     
    "managed"     : False,                                                      
    "custom_deps" : {                                                           
    },                                                                          
    "safesync_url": "",                                                         
  },                     
]
"""

* gclient sync

* Edit .gclient file and remove the "pdfium" solution.

* gclient sync


The command fails with:

Error: Command 'git merge-base HEAD origin' returned non-zero exit status 1 in /repos/tmp/repos/pdfium/buildtools/third_party/libc++/trunk



Any ideas?