diff --git a/spec/project/select-modules-in-sources.spec.ts b/spec/project/select-modules-in-sources.spec.ts
index 96b9508d..c5c84f70 100644
--- a/spec/project/select-modules-in-sources.spec.ts
+++ b/spec/project/select-modules-in-sources.spec.ts
@@ -182,6 +182,53 @@ describe('selectModulesInProjectSource', () => {
             expect(result.getModel().modules).to.deep.equal([]);
         });
 
+        it('removes files that become comment-only', () => {
+            const project = new Project({
+                sources: [
+                    new ProjectSource(
+                        'modules.json',
+                        JSON.stringify({
+                            modules: ['module1', 'module2', 'module3', 'extra1', 'extra2'],
+                        }),
+                    ),
+                    gql`
+                        # a comment in the keeper file
+                        type Keeper @rootEntity @modules(in: "module1", includeAllFields: true) {
+                            key: String @key
+                        }
+                    `.loc!.source,
+                    gql`
+                        # a comment in the discard file
+                        type Discard @rootEntity @modules(in: "extra2", includeAllFields: true) {
+                            key: String @key
+                        }
+                    `.loc!.source,
+                    // will also remove this one because we're throwing away comment-only file when
+                    // parsing a project. Documenting that behavior in this test case, but it's
+                    // probably fine either way
+                    {
+                        name: 'empty.graphqls',
+                        body: "# a file that's already comment-only",
+                    },
+                ],
+                modelOptions: { withModuleDefinitions: true },
+            });
+            expectToBeValid(project);
+
+            const result = project.withModuleSelection(['module1', 'module2'], {
+                removeModuleDeclarations: true,
+            });
+            expectToBeValid(result);
+            expect(result.sources.map((s) => s.body)).to.deep.equal([
+                `
+                        # a comment in the keeper file
+                        type Keeper @rootEntity  {
+                            key: String @key
+                        }
+                    `,
+            ]);
+        });
+
         it('removes the modules part in an object file with modules and something else', () => {
             const project = new Project({
                 sources: [
@@ -207,6 +254,85 @@ describe('selectModulesInProjectSource', () => {
 }`);
             expect(result.getModel().modules).to.deep.equal([]);
         });
+
+        it('works in a more complicated case', () => {
+            const result = run(
+                gql`
+                    # The IciDocument is deprecated because it will be replaced by general DocumentMeta - DocumentContent structure
+                    type IciDocument
+                        @rootEntity #(permissionProfile: "users")
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        id: ID @key
+
+                        accessGroup: String
+
+                        name: String
+                        mimeType: String
+
+                        "The base64 encoded binary contents"
+                        body: String
+                    }
+
+                    type InternationalCustomsData
+                        @suppress(warnings: UNUSED)
+                        @entityExtension
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        requestData: InternationalCustomsRequestData
+                        resultData: InternationalCustomsResultData
+                    }
+
+                    type InternationalCustomsRequestData
+                        @entityExtension
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        isInternationalCustomsRelevant: Boolean
+                            @defaultValue(value: false)
+                            @suppress(infos: NO_TYPE_CHECKS)
+                    }
+
+                    type InternationalCustomsResultData
+                        @entityExtension
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        internationalCustomsTransmittedTS: DateTime
+                        iciConsignmentId: String
+                        iciDeclarationId: String
+                        customsRegistrationNumber: String
+                        attachments: [IciAttachments]
+                    }
+
+                    type IciAttachments
+                        @valueObject
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        attachmentId: ID
+                        attachment: IciDocument @reference(keyField: "attachmentId")
+                    }
+
+                    # Used by app ici-result-sync to control sync status with ici.
+                    type SyncId
+                        @rootEntity
+                        @modules(in: ["module1", "module2"], includeAllFields: true) {
+                        systemKey: String @key
+                        syncId: String
+                    }
+                `,
+                [],
+                { removeModuleDeclarations: true },
+            );
+            expect(result).to.equal(`
+                    type OneAndTwo @rootEntity  {
+                        all: String 
+                        two: String 
+                        extra1: String 
+                        
+                    }
+
+                    type Two @rootEntity  {
+                        all: String 
+                        one: String 
+                    }
+
+                    
+                `);
+        });
     });
 });
 
diff --git a/src/project/select-modules-in-sources.ts b/src/project/select-modules-in-sources.ts
index 81c6ce45..e09ac0d3 100644
--- a/src/project/select-modules-in-sources.ts
+++ b/src/project/select-modules-in-sources.ts
@@ -21,6 +21,7 @@ import { findDirectiveWithName } from '../schema/schema-utils';
 import { Project, ProjectOptions } from './project';
 import { ProjectSource } from './source';
 import { isReadonlyArray } from '../utils/utils';
+import { isCommentOnlySource } from '../graphql/is-comment-only-source';
 
 export interface ModuleSelectionOptions {
     /**
@@ -255,6 +256,10 @@ function selectModulesInGraphQLSource({
         }
     }
 
+    if (!changes) {
+        return source.body;
+    }
+
     let currentPosition = 0;
     let output = '';
     for (let i = 0; i <= changes.length; i++) {
@@ -275,6 +280,11 @@ function selectModulesInGraphQLSource({
         }
     }
 
+    // if we removed everything except comments, delete the file
+    if (isCommentOnlySource(output)) {
+        return undefined;
+    }
+
     return output;
 }