diff --git a/flow-devloop-daemon/src/main/java/com/vaadin/flow/devloop/daemon/Compile.java b/flow-devloop-daemon/src/main/java/com/vaadin/flow/devloop/daemon/Compile.java
index 38a2e93b5c6..f1c6edf3c9c 100644
--- a/flow-devloop-daemon/src/main/java/com/vaadin/flow/devloop/daemon/Compile.java
+++ b/flow-devloop-daemon/src/main/java/com/vaadin/flow/devloop/daemon/Compile.java
@@ -432,8 +432,30 @@ void forgetResources(List<Path> resources) {
 
     /** Seeds the fingerprints, so an untouched project reports no changes. */
     void seedResources() {
+        seedResources(Long.MAX_VALUE);
+    }
+
+    /**
+     * Seeds the fingerprints of the resources the running application can have
+     * read.
+     * <p>
+     * The same bound {@link #seedFromDisk(long, long)} puts on sources, and for
+     * a sharper reason: a startup-only resource has no other way back into a
+     * change-set. The re-resolve that rebuilds the baseline after a pom edit
+     * has also copied the file onto the classpath, so its copy is current, and
+     * a baseline that took the edit as acted on would report "no changes" for a
+     * config the running JVM never loaded - on this apply and every later one.
+     *
+     * @param startedAtMillis
+     *            when the running application was launched
+     */
+    void seedResources(long startedAtMillis) {
         notified.clear();
-        forEachResource((module, source, stamp) -> notified.put(source, stamp));
+        forEachResource((module, source, stamp) -> {
+            if (stamp.modified() <= startedAtMillis) {
+                notified.put(source, stamp);
+            }
+        });
     }
 
     /**
@@ -902,7 +924,7 @@ void seedFromDisk(long startedAtMillis, long frontendCutoffMillis) {
                 applied.put(source, stamp);
             }
         });
-        seedResources();
+        seedResources(startedAtMillis);
         // Load-bearing for the frontend leg, not just tidiness: a bundled
         // frontend edit escalates to a restart, the restart re-registers, and
         // this runs again. Without it the same file would be offered after the
diff --git a/flow-devloop-daemon/src/test/java/com/vaadin/flow/devloop/daemon/CompileTest.java b/flow-devloop-daemon/src/test/java/com/vaadin/flow/devloop/daemon/CompileTest.java
index 1793637984b..b29f9a01507 100644
--- a/flow-devloop-daemon/src/test/java/com/vaadin/flow/devloop/daemon/CompileTest.java
+++ b/flow-devloop-daemon/src/test/java/com/vaadin/flow/devloop/daemon/CompileTest.java
@@ -596,6 +596,40 @@ public class Main { }
         assertEquals(List.of(config), changes.startup().modified());
     }
 
+    @Test
+    void staleResources_seedingKeepsAnEditMadeSinceTheAppStarted()
+            throws IOException {
+        // A pom edit re-seeds the baseline while the app runs, and the Maven
+        // re-resolve before it has already copied the edited config onto the
+        // classpath. Taking that edit as acted on would report "no changes"
+        // for a config the running JVM never loaded, and no later apply could
+        // see it again.
+        Reactor.Module app = module("app", "Main", """
+                package app;
+                public class Main { }
+                """);
+        Path config = write("app/src/main/resources/application.properties",
+                "server.port=8080");
+        Path served = write(
+                "app/src/main/resources/META-INF/resources/site.css", "body{}");
+        Compile compile = new Compile(project(app));
+        compile.copyResources(List.of(served));
+        long appStarted = System.currentTimeMillis();
+        touch("app/src/main/resources/application.properties");
+        // What the re-resolve's process-resources leaves behind: a copy at
+        // least as new as its source.
+        compile.copyResources(List.of(config));
+        touch("app/target/classes/application.properties");
+
+        compile.seedFromDisk(appStarted, appStarted);
+
+        Compile.ResourceChanges changes = compile.staleResources();
+        assertEquals(List.of(config), changes.startup().modified());
+        // What the app did start with is still seeded, or every apply would
+        // report every resource.
+        assertTrue(changes.live().isEmpty());
+    }
+
     @Test
     void staleResources_reportADeletedResourceTheWalkCannotSee()
             throws IOException {