Upon updating/bumping up the version and the build # in Xcode version 9.1, I saw the following upon doing git diff
diff --git a/star.xcodeproj/project.pbxproj b/star.xcodeproj/project.pbxproj
index c4601526..8fa3c762 100644
--- a/star.xcodeproj/project.pbxproj
+++ b/star.xcodeproj/project.pbxproj
@@ -767,7 +767,7 @@
- F4487BE11FB28C400079BAAD /* BuildFile in Sources */ = {isa = PBXBuildFile; };
+ F4487BE11FB28C400079BAAD /* (null) in Sources */ = {isa = PBXBuildFile; };
@@ -5625,7 +5625,7 @@
isa = PBXSourcesBuildPhase;
buildActionMask = 2147483647;
files = (
- F4487BE11FB28C400079BAAD /* BuildFile in Sources */,
+ F4487BE11FB28C400079BAAD /* (null) in Sources */,);
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
- <string>2.11.4</string>
+ <string>2.11.5</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleURLTypes</key>
@@ -39,7 +39,7 @@
</dict>
</array>
<key>CFBundleVersion</key>
- <string>02110400</string>
+ <string>02110500</string>
<key>FacebookAppID</key>
<string>70858204300</string>
<key>FacebookBetaAppID</key>
All I did was bump up the version of the project. But upon doing a git status and a git diff, I see some null references in the .pbxproj file. Has anybody else seen this. As a side-note we also use Cocoapods in our project.

I removed all (null) references in project file and all IDs which mentioned with them. Then tried to build run and archive App - all worked fine. Looks like Xcode did not removed them itself by some reason.
In your case try to remove F4487BE11FB28C400079BAAD with (null), and all lines with this F4487BE11FB28C400079BAAD too. And do this with other (null) references.