diff --git a/src/CodeCoverage.php b/src/CodeCoverage.php
index 6eccd3b93..9a92b91b1 100644
--- a/src/CodeCoverage.php
+++ b/src/CodeCoverage.php
@@ -108,13 +108,6 @@ final class CodeCoverage
      */
     private $parentClassesExcludedFromUnintentionallyCoveredCodeCheck = [];
 
-    /**
-     * Determine if the data has been initialized or not.
-     *
-     * @var bool
-     */
-    private $isInitialized = false;
-
     /**
      * @var ?CoveredFileAnalyser
      */
@@ -151,10 +144,9 @@ public function getReport(): Directory
      */
     public function clear(): void
     {
-        $this->isInitialized = false;
-        $this->currentId     = null;
-        $this->data          = new ProcessedCodeCoverageData;
-        $this->tests         = [];
+        $this->currentId = null;
+        $this->data      = new ProcessedCodeCoverageData;
+        $this->tests     = [];
     }
 
     /**
@@ -170,8 +162,12 @@ public function filter(): Filter
      */
     public function getData(bool $raw = false): ProcessedCodeCoverageData
     {
-        if (!$raw && $this->includeUncoveredFiles) {
-            $this->addUncoveredFilesFromFilter();
+        if (!$raw) {
+            if ($this->processUncoveredFiles) {
+                $this->processUncoveredFilesFromFilter();
+            } elseif ($this->includeUncoveredFiles) {
+                $this->addUncoveredFilesFromFilter();
+            }
         }
 
         return $this->data;
@@ -212,10 +208,6 @@ public function start($id, bool $clear = false): void
             $this->clear();
         }
 
-        if ($this->isInitialized === false) {
-            $this->initializeData();
-        }
-
         $this->currentId = $id;
 
         $this->driver->start();
@@ -510,7 +502,7 @@ private function addUncoveredFilesFromFilter(): void
     {
         $uncoveredFiles = array_diff(
             $this->filter->files(),
-            array_keys($this->data->lineCoverage())
+            $this->data->coveredFiles()
         );
 
         foreach ($uncoveredFiles as $uncoveredFile) {
@@ -526,6 +518,29 @@ private function addUncoveredFilesFromFilter(): void
         }
     }
 
+    /**
+     * @throws UnintentionallyCoveredCodeException
+     */
+    private function processUncoveredFilesFromFilter(): void
+    {
+        $uncoveredFiles = array_diff(
+            $this->filter->files(),
+            $this->data->coveredFiles()
+        );
+
+        $this->driver->start();
+
+        foreach ($this->filter->files() as $file) {
+            foreach ($uncoveredFiles as $uncoveredFile) {
+                if (file_exists($uncoveredFile)) {
+                    include_once $file;
+                }
+            }
+        }
+
+        $this->append($this->driver->stop(), self::UNCOVERED_FILES);
+    }
+
     /**
      * @throws UnintentionallyCoveredCodeException
      * @throws ReflectionException
@@ -628,36 +643,6 @@ private function processUnintentionallyCoveredUnits(array $unintentionallyCovere
         return array_values($unintentionallyCoveredUnits);
     }
 
-    /**
-     * @throws UnintentionallyCoveredCodeException
-     */
-    private function initializeData(): void
-    {
-        $this->isInitialized = true;
-
-        if ($this->processUncoveredFiles) {
-            // by collecting dead code data here on an initial pass, future runs with test data do not need to
-            if ($this->driver->canDetectDeadCode()) {
-                $this->driver->enableDeadCodeDetection();
-            }
-
-            $this->driver->start();
-
-            foreach ($this->filter->files() as $file) {
-                if ($this->filter->isFile($file)) {
-                    include_once $file;
-                }
-            }
-
-            // having now collected dead code for the entire list of files, we can safely skip this data on subsequent runs
-            if ($this->driver->canDetectDeadCode()) {
-                $this->driver->disableDeadCodeDetection();
-            }
-
-            $this->append($this->driver->stop(), self::UNCOVERED_FILES);
-        }
-    }
-
     private function coveredFileAnalyser(): CoveredFileAnalyser
     {
         if ($this->coveredFileAnalyser !== null) {