diff --git a/olex2/README.md b/olex2/README.md
index 52bcfc3..325ba0f 100644
--- a/olex2/README.md
+++ b/olex2/README.md
@@ -79,7 +79,11 @@ executable and must match its libc. So the recipe:
 
 - ships glibc 2.39 + GCC 14 `libstdc++`/`libgcc_s` under `$PREFIX/sysroot`
   (frozen Fedora 40 rpms from kojipkgs, Fedora's permanent build archive;
-  same glibc generation as the upstream build host);
+  same glibc generation as the upstream build host). glibc and libstdc++
+  unpack to `usr/lib64`, libgcc to `/lib64` (Fedora relies on the
+  filesystem package's `lib64 -> usr/lib64` symlink, which we do not
+  extract), so `configure` merges `lib64` into `usr/lib64` and recreates
+  the symlink — one lib dir for the RPATH;
 - runs `patchelf --set-interpreter <sysroot ld.so> --force-rpath --set-rpath
   <sysroot libdir>:$PREFIX/lib:$PREFIX/ilib:$PREFIX/cctbx/cctbx_build/lib:$PREFIX:$ORIGIN`
   on every dynamic executable (`hart`, `hart_mpi` are static and skipped).
diff --git a/olex2/build b/olex2/build
index 1010926..27b9a8a 100755
--- a/olex2/build
+++ b/olex2/build
@@ -40,17 +40,23 @@ OLEX2_PATCH_EXES=(olex2c olex2 unirun NoSpherA2 hart_mpi)
 
 pbuild::configure() {
     local -r zip="${SRC_DIR}/olex2-${V}-linux64.zip"
-    [[ -s "${zip}" ]] || std::die 42 "olex2: ${zip} not found - prep did not fetch it. \
-Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) and re-run."
-    command -v unzip >/dev/null || std::die 42 "olex2: 'unzip' not on PATH on this build host"
-    # partial downloads reused from distfiles are the classic failure: test the archive first
-    unzip -tq "${zip}" >/dev/null || \
-        std::die 42 "olex2: archive is corrupt/truncated - rm <distdir>/olex2-${V}-linux64.zip and re-run"
-    # ~1 GB unpacked (cctbx + python + sample data); SRC_DIR is under --tmpdir
-    unzip -q -o "${zip}" -d "${SRC_DIR}" || std::die 42 "olex2: unzip failed (disk/quota at --tmpdir?)"
-    [[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]] || \
-        std::die 42 "olex2: unexpected archive layout - expected ${SRC_DIR}/olex2/{olex2,olex2c}"
-    rm -f "${zip}"
+    if [[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]]; then
+        # re-run after a failed configure/install: prep's stamp is set, the
+        # tree is already unpacked - reuse it (the zip may be gone from SRC_DIR)
+        echo "olex2: reusing unpacked tree in ${SRC_DIR}/olex2"
+    else
+        [[ -s "${zip}" ]] || std::die 42 "olex2: ${zip} not found - prep did not fetch it. \
+Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) and re-run (-f)."
+        command -v unzip >/dev/null || std::die 42 "olex2: 'unzip' not on PATH on this build host"
+        # partial downloads reused from distfiles are the classic failure: test the archive first
+        unzip -tq "${zip}" >/dev/null || \
+            std::die 42 "olex2: archive is corrupt/truncated - rm <distdir>/olex2-${V}-linux64.zip and re-run"
+        # ~1 GB unpacked (cctbx + python + sample data); SRC_DIR is under --tmpdir
+        unzip -q -o "${zip}" -d "${SRC_DIR}" || std::die 42 "olex2: unzip failed (disk/quota at --tmpdir?)"
+        [[ -f "${SRC_DIR}/olex2/olex2c" && -f "${SRC_DIR}/olex2/olex2" ]] || \
+            std::die 42 "olex2: unexpected archive layout - expected ${SRC_DIR}/olex2/{olex2,olex2c}"
+        rm -f "${zip}"   # 255 MB copy; the distfiles cache keeps the original
+    fi
 
     # --- private glibc 2.39 + libstdc++ 14 sysroot (Fedora 40 rpms) ----------
     command -v rpm2cpio >/dev/null && command -v cpio >/dev/null || \
@@ -64,6 +70,15 @@ Pre-stage the archive by hand as <distdir>/olex2-${V}-linux64.zip (see README) a
         ( cd "${sysroot}" && rpm2cpio "${SRC_DIR}/${rpm}" | cpio -idm --quiet ) || \
             std::die 42 "olex2: extracting ${rpm} failed"
     done
+    # Fedora's glibc + libstdc++ install to /usr/lib64 but libgcc still to
+    # /lib64, which on a real system is the filesystem package's symlink to
+    # usr/lib64 - we do not extract that package, so recreate the merge here.
+    if [[ -d "${sysroot}/lib64" && ! -L "${sysroot}/lib64" ]]; then
+        mkdir -p "${sysroot}/usr/lib64"
+        cp -r --preserve=mode,timestamps,links "${sysroot}/lib64/." "${sysroot}/usr/lib64/" && \
+            rm -rf "${sysroot}/lib64" && ln -s usr/lib64 "${sysroot}/lib64" || \
+            std::die 42 "olex2: merging sysroot/lib64 into sysroot/usr/lib64 failed"
+    fi
     local ld libc libdir
     ld="$(find "${sysroot}" -type f -name 'ld-linux-x86-64.so.2' -print -quit)"
     libc="$(find "${sysroot}" -type f -name 'libc.so.6' -print -quit)"