diff --git a/Library/Homebrew/cmd/nodenv-sync.rb b/Library/Homebrew/cmd/nodenv-sync.rb
index f57050e06f..5ae54f19ad 100644
--- a/Library/Homebrew/cmd/nodenv-sync.rb
+++ b/Library/Homebrew/cmd/nodenv-sync.rb
@@ -58,6 +58,8 @@ module Homebrew
         (0..minor_version).each do |minor|
           (0..patch_version).each do |patch|
             link_path = nodenv_versions/"#{major_version}.#{minor}.#{patch}"
+            # Don't clobber existing user installations.
+            next if link_path.exist? && !link_path.symlink?
 
             FileUtils.rm_f link_path
             FileUtils.ln_sf path, link_path
diff --git a/Library/Homebrew/cmd/pyenv-sync.rb b/Library/Homebrew/cmd/pyenv-sync.rb
index c9a7c18e24..2ae2b8ca09 100644
--- a/Library/Homebrew/cmd/pyenv-sync.rb
+++ b/Library/Homebrew/cmd/pyenv-sync.rb
@@ -56,6 +56,8 @@ module Homebrew
 
         (0..patch_version).each do |patch|
           link_path = pyenv_versions/"#{major_version}.#{minor_version}.#{patch}"
+          # Don't clobber existing user installations.
+          next if link_path.exist? && !link_path.symlink?
 
           FileUtils.rm_f link_path
           FileUtils.ln_sf path, link_path
diff --git a/Library/Homebrew/cmd/rbenv-sync.rb b/Library/Homebrew/cmd/rbenv-sync.rb
index bf2bbf9338..4a9bf777d1 100644
--- a/Library/Homebrew/cmd/rbenv-sync.rb
+++ b/Library/Homebrew/cmd/rbenv-sync.rb
@@ -57,6 +57,8 @@ module Homebrew
 
         (0..patch_version).each do |patch|
           link_path = rbenv_versions/"#{major_version}.#{minor_version}.#{patch}"
+          # Don't clobber existing user installations.
+          next if link_path.exist? && !link_path.symlink?
 
           FileUtils.rm_f link_path
           FileUtils.ln_sf path, link_path