custom-scripts/scripts/pre_remove_40_find_unowned_lib_links

 #!/bin/sh
 set -e
 
-for libdir in /lib /usr/lib /lib/*-gnu* /usr/lib/*-gnu*
+for prefix in / /usr/
+do
+  for lib in "${prefix}lib" "${prefix}lib32" "${prefix}lib64" "${prefix}libx32"
+  do
+    test -d "$lib" || continue
+    test -L "$lib" && continue
+    for libdir in "$lib" "$lib"/*-gnu*
     do
 	test -d "$libdir" || continue
 	for f in "$libdir"/*
 	do
-		test ! -d "$f" || continue
+		test -d "$f" && continue
 		test -L "$f" || continue
 		rl=$(readlink "$f")
 		test -n "${rl##/etc/alternatives/*}" || continue
-		if ! dpkg-query -S "$f" >/dev/null 2>&1
+		owned=0
+		dpkg-query -S "$f" >/dev/null 2>&1 && owned=1
+		if [ "$owned" = "0" ] && [ -L "/lib" ]
+		then
+			dpkg-query -S "${f#/usr}" >/dev/null 2>&1 && owned=1
+		fi
+		if [ "$owned" = "0" ]
 		then
 			case "$f" in
 				/lib/ld-lsb.so.?)
@@ -40,3 +52,5 @@ do
 		fi
 	done
     done
+  done
+done

debian/changelog

@@ -30,6 +30,8 @@ piuparts (0.99) UNRELEASED; urgency=medium
   * scripts/post_distupgrade_exceptions:
     - Handle /var/lib/pam/seen stretch -> buster upgrade by running
       pam-auth-update if needed. Workaround for #920760.
+  * scripts/pre_remove_40_find_unowned_lib_links:
+    - Handle --merged-usr environments.
   * master-bin/reschedule_piuparts_tests: Do not act on 'bugged/*.log' and
     'affected/*.log' by default. Add --bugged, --affected flags.
 

instances/piuparts.conf-template.pejacevic

@@ -268,7 +268,7 @@ piuparts-flags =
 	%(flags-default)s
 distro = None
 upgrade-test-distros = sid
-chroot-tgz = %(upgrade-test-distros)s-merged-usr_%(arch)s.tgz
+chroot-tgz = %(upgrade-test-distros)s-merged-usr_@ARCH@.tgz
 # 3 days (60*60*24*3)
 max-tgz-age = 259200
 
@@ -390,7 +390,7 @@ piuparts-flags =
 	--merged-usr
 	%(flags-default)s
 distro = sid
-chroot-tgz = %(distro)s-merged-usr_%(arch)s.tgz
+chroot-tgz = %(distro)s-merged-usr_@ARCH@.tgz
 
 
 [sid-broken-symlinks]