diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2f05953158..3a9ba175c9 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -336,7 +336,15 @@ else
         if [ -f ${easystack_file} ]; then
             echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 
-            ${EB} --easystack ${easystack_file} --robot
+            if [[ ${easystack_file} == *"/rebuilds/"* ]]; then
+                # the removal script should have removed the original directory and created a new and empty one
+                # to work around permission issues:
+                # https://github.com/EESSI/software-layer/issues/556
+                echo_yellow "This is a rebuild, so using --try-amend=keeppreviousinstall=True to reuse the already created directory"
+                ${EB} --easystack ${easystack_file} --robot --try-amend=keeppreviousinstall=True
+            else
+                ${EB} --easystack ${easystack_file} --robot
+            fi
             ec=$?
 
             # copy EasyBuild log file if EasyBuild exited with an error
diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1a03a7af98..e4b377fd16 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -125,13 +125,18 @@ if [ $EUID -eq 0 ]; then
                     # Two dirname invocations, so returns e.g. /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2
                     app_installprefix=$(dirname $(dirname ${app_modulepath}))
                     app_dir=${app_installprefix}/software/${app}
+                    app_subdirs=$(find ${app_dir} -mindepth 1 -maxdepth 1 -type d)
                     app_module=${app_installprefix}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    # recreate some directory to work around permission denied
-                    # issues when rebuilding the package
-                    mkdir -p ${app_dir}/easybuild
+                    # recreate the installation directories and first-level subdirectories to work around permission denied
+                    # issues when rebuilding the package (see https://github.com/EESSI/software-layer/issues/556)
+                    echo_yellow "Recreating an empty ${app_dir}..."
+                    mkdir -p ${app_dir}
+                    for app_subdir in ${app_subdirs}; do
+                        mkdir -p ${app_subdir}
+                    done
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"
diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20250121-eb-4.9.4-SciPy-bundle-2023.07-bug-fixes.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20250121-eb-4.9.4-SciPy-bundle-2023.07-bug-fixes.yml
new file mode 100644
index 0000000000..f7db7a994c
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20250121-eb-4.9.4-SciPy-bundle-2023.07-bug-fixes.yml
@@ -0,0 +1,14 @@
+# 2025.01.21
+# While adding support for Intel Sapphire Rapids, additional patches applied to the
+# original easyconfig were required to successfully build SciPy-bundle 2023.07.
+# In order to keep the stack consistent across the different CPUs,
+# a rebuild is done for all CPU targets with this updated easyconfig.
+# See:
+# - https://github.com/easybuilders/easybuild-easyconfigs/pull/19419
+# - https://github.com/easybuilders/easybuild-easyconfigs/pull/20817
+# - https://github.com/easybuilders/easybuild-easyconfigs/pull/21693
+easyconfigs:
+  - SciPy-bundle-2023.07-gfbf-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21693
+        from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0