diff --git a/src/classify-module.ts b/src/classify-module.ts
index 291a647..114b420 100644
--- a/src/classify-module.ts
+++ b/src/classify-module.ts
@@ -21,10 +21,13 @@ const readPJType = cachedMtime(
   })
 )
 
-export const classifyModule = (fileName: string): PackageJsonType | 'json' => {
+export const classifyModule = (
+  fileName: string
+): PackageJsonType | 'json' => {
   if (fileName.endsWith('.json')) {
     return 'json'
-  } if (fileName.endsWith('.cts') || fileName.endsWith('.cjs')) {
+  }
+  if (fileName.endsWith('.cts') || fileName.endsWith('.cjs')) {
     return 'commonjs'
   } else if (fileName.endsWith('.mts') || fileName.endsWith('.mjs')) {
     return 'module'
diff --git a/src/service/get-output-typecheck.ts b/src/service/get-output-typecheck.ts
index c71bd8d..e5b6948 100644
--- a/src/service/get-output-typecheck.ts
+++ b/src/service/get-output-typecheck.ts
@@ -1,8 +1,9 @@
 // Get output with full type-checking from the LanguageService.
 
 import { relative } from 'path'
-import type ts from 'typescript'
+import ts from 'typescript'
 import { info, warn } from '../debug.js'
+import { readFile } from '../ts-sys-cached.js'
 import { addRootFile, updateFileVersion } from './file-versions.js'
 import { getLanguageService } from './language-service.js'
 import { markFileNameInternal } from './resolve-module-name-literals.js'
@@ -27,6 +28,30 @@ export const getOutputTypeCheck = (
   markFileNameInternal(fileName)
   updateFileVersion(fileName, code)
 
+  // TODO: It's not clear which fields on dependenciesInfo are relevant
+  // TODO: Ensure that preProcessFile looks for dependencies recursively
+  // TODO: Skip the step of putting the fileNames into a Set if it's
+  //       guaranteed that a given file won't be listed multiple times
+  const {
+    referencedFiles,
+    typeReferenceDirectives,
+    libReferenceDirectives,
+    importedFiles,
+  } = ts.preProcessFile(code)
+  const dependencyFileNames = new Set<string>()
+  for (const file of [
+    ...referencedFiles,
+    ...typeReferenceDirectives,
+    ...libReferenceDirectives,
+    ...importedFiles,
+  ]) {
+    dependencyFileNames.add(file.fileName)
+  }
+
+  for (const dependencyFileName of dependencyFileNames) {
+    updateFileVersion(dependencyFileName, readFile(fileName) || '')
+  }
+
   // if we can't get the source file, then return the code un-compiled.
   // Eg, loading a JS file if allowJs is not set.
   const programBefore = service.getProgram()
diff --git a/src/service/load.ts b/src/service/load.ts
index c5c13d2..f5d6f0b 100644
--- a/src/service/load.ts
+++ b/src/service/load.ts
@@ -3,7 +3,7 @@
 import { cachedMtime } from '@isaacs/cached'
 import { mkdirSync, writeFileSync } from 'fs'
 import { relative, resolve } from 'path'
-import { ParsedCommandLine } from 'typescript'
+import { Diagnostic, ParsedCommandLine } from 'typescript'
 import { info } from '../debug.js'
 import { getOutputFile } from '../get-output-file.js'
 import {
@@ -31,30 +31,40 @@ export const load = (
   const config = tsconfig()
 
   if (lastConfig && config !== lastConfig) {
-    compileTypeCheck.cache.clear()
     compileTranspileOnly.cache.clear()
-    compileTypeCheck.mtimeCache.clear()
     compileTranspileOnly.mtimeCache.clear()
   }
   lastConfig = config
 
-  // compile to a file on disk, but only if the source has changed.
-  const compile = typeCheck ? compileTypeCheck : compileTranspileOnly
-  const cachedMtime = compile.mtimeCache.get(fileName)?.[0]
-  const newMtime = compile.getMtime(fileName)
+  let compile: (fileName: string) => {
+    outputText: string | undefined
+    diagnostics: Diagnostic[]
+  }
   const outFile = getOutputFile(fileName)
-  const cachedResult = compile.cache.get(fileName)
 
-  if (
-    cachedMtime &&
-    cachedMtime === newMtime &&
-    fileExists(outFile) &&
-    cachedResult
-  ) {
-    // saw this one, and have previous build available
-    return {
-      fileName: outFile,
-      diagnostics: reportAll(cachedResult.diagnostics, pretty),
+  // TODO: Re-enable caching of type-checked results
+  if (typeCheck) {
+    compile = compileTypeCheck
+  } else {
+    let cachedCompile = compileTranspileOnly
+    compile = cachedCompile
+
+    // Skip compiling if the source has not changed
+    const cachedMtime = cachedCompile.mtimeCache.get(fileName)?.[0]
+    const newMtime = cachedCompile.getMtime(fileName)
+    const cachedResult = cachedCompile.cache.get(fileName)
+
+    if (
+      cachedMtime &&
+      cachedMtime === newMtime &&
+      fileExists(outFile) &&
+      cachedResult
+    ) {
+      // saw this one, and have previous build available
+      return {
+        fileName: outFile,
+        diagnostics: reportAll(cachedResult.diagnostics, pretty),
+      }
     }
   }
 
@@ -82,12 +92,19 @@ export const load = (
   }
 }
 
-const compileTypeCheck = cachedMtime((fileName: string) => {
+// It's fine to cache the results of transpilation, as compileTranspileOnly does,
+// but it's not safe for this function to perform caching based purely on the
+// mtime of a single source file. A dependency may have (for example)
+// deleted something that the file was referencing.
+// TODO: Cache compile results based on the mtime of all affected files,
+//       not just the one we're currently getting the results for
+//       (update cachedMtime() to accept an array of paths)
+const compileTypeCheck = (fileName: string) => {
   const normalizedFileName: string = normalizeSlashes(fileName)
   /* c8 ignore next */
   const content = readFile(fileName) || ''
   return compile(content, normalizedFileName, true)
-})
+}
 
 const compileTranspileOnly = cachedMtime((fileName: string) => {
   const normalizedFileName: string = normalizeSlashes(fileName)