diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3dd5aba0..f531668d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Record map classes and their generated data classes are now automatically added to source control (#955)
 
+### Fixed
+- Import All no longer deletes items that are mapped in from another database, which could delete Embedded Git itself where it is mapped instance-wide (#997)
+
 ## [2.17.1] - 2026-08-18
 
 ### Fixed
diff --git a/cls/SourceControl/Git/Utils.cls b/cls/SourceControl/Git/Utils.cls
index 240cfbad..d2bb11f3 100644
--- a/cls/SourceControl/Git/Utils.cls
+++ b/cls/SourceControl/Git/Utils.cls
@@ -1752,12 +1752,16 @@ ClassMethod ImportRoutines(force As %Boolean = 0, pullEventClass As %String) As
         set externalName = ..ExternalName(item)
         set fullExternalName = ..FullExternalName(item)
         if '##class(%File).Exists(fullExternalName) {
-            write !,fullExternalName," does not exist - deleting ",item
-            set modification = ##class(SourceControl.Git.Modification).%New()
-            set modification.changeType = "D"
-            set modification.internalName = item
-            set modification.externalName = externalName
-            set files($increment(files)) = modification
+            if ##class(%Library.RoutineMgr).IsMapped(item) {
+                write !,fullExternalName," does not exist, but ",item," is mapped in from another database - not deleting it"
+            } else {
+                write !,fullExternalName," does not exist - deleting ",item
+                set modification = ##class(SourceControl.Git.Modification).%New()
+                set modification.changeType = "D"
+                set modification.internalName = item
+                set modification.externalName = externalName
+                set files($increment(files)) = modification
+            }
         }
     }
 
diff --git a/test/UnitTest/SourceControl/Git/MappedItem.cls b/test/UnitTest/SourceControl/Git/MappedItem.cls
new file mode 100644
index 00000000..d3b072a1
--- /dev/null
+++ b/test/UnitTest/SourceControl/Git/MappedItem.cls
@@ -0,0 +1,84 @@
+/// Tests that items mapped in from another database are left alone by Import All.
+/// Deleting such an item removes it from the database it is mapped from, and so from every namespace that
+/// maps it in - that is how Embedded Git, mapped instance-wide, deleted itself.
+/// See https://github.com/intersystems/git-source-control/issues/997 .
+Class UnitTest.SourceControl.Git.MappedItem Extends UnitTest.SourceControl.Git.AbstractTest
+{
+
+/// Package mapped in from the %SYS namespace's routine database for the duration of the test.
+Parameter MappedPackage As STRING = "gitunittestmapped";
+
+Parameter MappedClass As STRING = "gitunittestmapped.TestClass";
+
+Property PackageMappingCreated As %Boolean [ InitialExpression = 0 ];
+
+Method %OnNew(initvalue) As %Status
+{
+	$$$QuitOnError(##super(initvalue))
+	// mapped items are read-only by default, which keeps them out of source control entirely;
+	// this test needs the mapped class tracked so that Import All considers deleting it
+	set settings = ##class(SourceControl.Git.Settings).%New()
+	set settings.mappedItemsReadOnly = 0
+	quit settings.%Save()
+}
+
+Method %OnClose() As %Status [ Private, ServerOnly = 1 ]
+{
+	// the class lives in the mapped database, so it has to go before the mapping that reaches it
+	if $$$defClassDefined(..#MappedClass) {
+		do $system.OBJ.Delete(..#MappedClass)
+	}
+	if ..PackageMappingCreated {
+		do ..DeletePackageMapping(..#MappedPackage)
+	}
+	quit ##super()
+}
+
+Method TestMappedClassNotDeleted()
+{
+	set internalName = ..#MappedClass_".CLS"
+
+	$$$ThrowOnError(..CreatePackageMapping(..#MappedPackage))
+	set ..PackageMappingCreated = 1
+
+	set classDef = ##class(%Dictionary.ClassDefinition).%New()
+	set classDef.Name = ..#MappedClass
+	$$$ThrowOnError(classDef.%Save())
+	$$$ThrowOnError($system.OBJ.Compile(..#MappedClass, "ck"))
+
+	// the class is stored in the %SYS namespace's database rather than this namespace's own
+	do $$$AssertTrue(##class(%Library.RoutineMgr).IsMapped(internalName), internalName_" is mapped in from another database")
+
+	do $$$AssertStatusOK(##class(SourceControl.Git.Utils).AddToSourceControl(internalName))
+	set fullExternalName = ##class(SourceControl.Git.Utils).FullExternalName(internalName)
+	do $$$AssertTrue(##class(%File).Exists(fullExternalName), "mapped class exported to "_fullExternalName)
+
+	// the situation that triggered #997: the item is in source control, but has no file on disk
+	do $$$AssertTrue(##class(%File).Delete(fullExternalName), "deleted "_fullExternalName)
+	do $$$AssertStatusOK(##class(SourceControl.Git.API).ImportAll(1))
+
+	do $$$AssertTrue($$$defClassDefined(..#MappedClass), ..#MappedClass_" still exists after Import All")
+}
+
+/// Creates a package mapping in %SYS so that classes in <var>package</var> are stored in the database
+/// the %SYS namespace keeps its routines in, rather than this namespace's own.
+Method CreatePackageMapping(package As %String) As %Status
+{
+	set ns = $namespace
+	new $namespace
+	set $namespace = "%SYS"
+	$$$QuitOnError(##class(Config.Namespaces).Get("%SYS", .namespaceProps))
+	set props("Database") = namespaceProps("Routines")
+	quit ##class(Config.MapPackages).Create(ns, package, .props)
+}
+
+/// Deletes the package mapping for <var>package</var>.
+ClassMethod DeletePackageMapping(package As %String) As %Status
+{
+	set ns = $namespace
+	new $namespace
+	set $namespace = "%SYS"
+	quit ##class(Config.MapPackages).Delete(ns, package)
+}
+
+}