diff --git a/icu4c/source/data/misc/miscfiles.mk b/icu4c/source/data/misc/miscfiles.mk
deleted file mode 100644
index 0c18119d47a..00000000000
--- a/icu4c/source/data/misc/miscfiles.mk
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright (C) 2016 and later: Unicode, Inc. and others.
-# License & terms of use: http://www.unicode.org/copyright.html
-# *   Copyright (C) 2003-2015, International Business Machines
-# *   Corporation and others.  All Rights Reserved.
-# A list of txt's to build
-# Note: 
-#
-#   If you are thinking of modifying this file, READ THIS. 
-#
-# Instead of changing this file [unless you want to check it back in],
-# you should consider creating a 'misclocal.mk' file in this same directory.
-# Then, you can have your local changes remain even if you upgrade or re-
-# configure ICU.
-#
-# Example 'misclocal.mk' files:
-#
-#  * To add an additional file to the list: 
-#    _____________________________________________________
-#    |  MISC_SOURCE_LOCAL =   myFile.txt ...
-#
-#  * To REPLACE the default list and only build a subset of files:
-#    _____________________________________________________
-#    |  MISC_SOURCE = zoneinfo.txt
-#
-#
-
-MISC_SOURCE = \
-zoneinfo64.txt supplementalData.txt likelySubtags.txt plurals.txt \
-numberingSystems.txt icuver.txt icustd.txt metadata.txt metaZones.txt \
-windowsZones.txt keyTypeData.txt timezoneTypes.txt currencyNumericCodes.txt \
-genderList.txt dayPeriods.txt pluralRanges.txt
diff --git a/icu4c/source/data/translit/trnsfiles.mk b/icu4c/source/data/translit/trnsfiles.mk
deleted file mode 100644
index 3c2630b8200..00000000000
--- a/icu4c/source/data/translit/trnsfiles.mk
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright (C) 2016 and later: Unicode, Inc. and others.
-# License & terms of use: http://www.unicode.org/copyright.html
-# *   Copyright (C) 1997-2006, International Business Machines
-# *   Corporation and others.  All Rights Reserved.
-# A list of txt's to build
-# Note: 
-#
-#   If you are thinking of modifying this file, READ THIS. 
-#
-# Instead of changing this file [unless you want to check it back in],
-# you should consider creating a 'trnslocal.mk' file in this same directory.
-# Then, you can have your local changes remain even if you upgrade or re
-# configure the ICU.
-#
-# Example 'trnslocal.mk' files:
-#
-#  * To add an additional transliterators to the list: 
-#    _____________________________________________________
-#    |  TRANSLIT_SOURCE_LOCAL =   myTranslitRules.txt ...
-#
-#  * To REPLACE the default list and only build with a few
-#     transliterators:
-#    _____________________________________________________
-#    |  TRANLIST_SOURCE = el.txt th.txt
-#
-#
-
-TRANSLIT_SOURCE=root.txt en.txt el.txt
diff --git a/tools/cldr/cldr-to-icu/build-icu-data.xml b/tools/cldr/cldr-to-icu/build-icu-data.xml
index 0f574bb903f..ea9e765f0d8 100644
--- a/tools/cldr/cldr-to-icu/build-icu-data.xml
+++ b/tools/cldr/cldr-to-icu/build-icu-data.xml
@@ -379,12 +379,26 @@
             </classpath>
         </taskdef>
 
+        <!-- If a directory is listed here, then every file in it is assumed to be automatically
+             generated by the conversion tool, unless it is explicitly listed in a <retain> element.
+             The tool then checks every file to determine if it has the expected header present,
+             indiciating that it was automatically generated, before deleting it.
+             
+             If unexpected files are found, the "clean" task will fail without deleting anything
+             (unless'forceDelete' is set to override this). Note that even if 'forceDelete' is set,
+             the files listed explicitly below will never be deleted by this process.
+
+             This two-step approach minimizes the risk that the conversion process will ever
+             accidentally delete a manually maintained file.             
+             -->
         <outputDirectories root="${outDir}" forceDelete="${forceDelete}">
             <dir name="brkitr">
                 <retain path="dictionaries"/>
                 <retain path="rules"/>
             </dir>
             <dir name="coll">
+                <!-- Legacy files whose file names aren't supported for automatic generation.
+                     Simple to maintain manually and unlikely to ever change again. -->
                 <retain path="de__PHONEBOOK.txt"/>
                 <retain path="de_.txt"/>
                 <retain path="es__TRADITIONAL.txt"/>
@@ -394,23 +408,25 @@
             <dir name="lang"/>
             <dir name="locales"/>
             <dir name="misc">
+                <!-- Machine generated files produced by different tools.
+                     Possibly worth moving into the new LDML conversion tool one day. -->
                 <retain path="currencyNumericCodes.txt"/>
-                <retain path="icudata.rc"/>
-                <retain path="icustd.txt"/>
                 <retain path="zoneinfo64.txt"/>
-                <!-- This file should be removed before the next release. -->
-                <retain path="miscfiles.mk"/>
+                <!-- Project file (not ICU data), unlikely to ever be auto-generated. -->
+                <retain path="icudata.rc"/>
+                <!-- Small high-level metadata file, stable and easy to maintain manually. -->
+                <retain path="icustd.txt"/>
             </dir>
             <dir name="rbnf"/>
             <dir name="region"/>
             <dir name="translit">
+                <!-- Small, easy to maintain, special case top-level files. -->
                 <retain path="en.txt"/>
                 <retain path="el.txt"/>
-                <!-- This file should be removed before the next release. -->
-                <retain path="trnsfiles.mk"/>
             </dir>
             <dir name="unit"/>
             <dir name="zone">
+                <!-- Manually edited to support TZ database name compatibility. -->
                 <retain path="tzdbNames.txt"/>
             </dir>
         </outputDirectories>