diff --git a/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp b/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
index a77c64fec..b49eb9b65 100644
--- a/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
+++ b/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
@@ -418,6 +418,23 @@ void RCore::buildMatchingMol() {
     // then keep one attachment
     if (atom->getAtomicNum() == 0 && atom->getDegree() == 1 &&
         isDummyRGroupAttachment(*atom)) {
+      // if we are a query in disguise, don't strip
+      if (atom->hasQuery()) {
+        auto q = atom->getQuery()->getDescription();
+        // If we are anything but AtomNull or AtomAtomicNum we are not
+        //  fully a dummy atom
+        if (q != "AtomNull" && q != "AtomAtomicNum") {
+          unsigned int type = 0xFFFFFFFF;
+          //  If we are were set as an RLABEL of type Isotope we probably
+          //   have a query of named "AtomIsotope"
+          //   we DO strip these unless they have an additional query
+          if (q != "AtomIsotope" || !atom->getPropIfPresent(RLABEL_TYPE, type) ||
+              type != RGroupLabels::IsotopeLabels) {
+            continue;
+          }
+        }
+      }
+
       // remove terminal user R groups and map the index of the core neighbor
       // atom to the index of the removed terminal R group
       const int neighborIdx = *matchingMol->getAtomNeighbors(atom).first;
diff --git a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
index 2dab6cb39..4b954aa19 100644
--- a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
+++ b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
@@ -4146,13 +4146,42 @@ void testRgroupDecompZipping() {
   }
 }
 
+void testSmartsOnDummyAtoms() {
+  BOOST_LOG(rdInfoLog)
+      << "********************************************************\n";
+  BOOST_LOG(rdInfoLog)
+      << "Test we can reconstruct rgroup decomps that break rings" << std::endl;
+
+  const auto core = "[$([1C]):1]C[$([2C]):2]"_smarts;
+    
+  const auto mol1 = "N[1C]C[2C]"_smiles;
+  const auto mol2 = "N[2C]C[1C]"_smiles;
+
+  const std::vector<std::string> expected = {
+    "Core:C([*:1])[*:2] R1:N[1C][*:1] R2:[2C][*:2]",
+    "Core:C([*:1])[*:2] R1:[1C][*:1] R2:N[2C][*:2]"
+  };
+
+  RGroupDecomposition decomp(*core);
+  auto add11 = decomp.add(*mol1);
+  TEST_ASSERT(add11 == 0);
+  add11 = decomp.add(*mol2);
+  TEST_ASSERT(add11 == 1)
+  decomp.process();
+  RGroupRows rows = decomp.getRGroupsAsRows();
+  int i = 0;
+  for (RGroupRows::const_iterator it = rows.begin(); it != rows.end();
+       ++it, ++i) {
+    CHECK_RGROUP(it, expected[i]);
+  }
+}
+
 int main() {
   RDLog::InitLogs();
   boost::logging::disable_logs("rdApp.debug");
   BOOST_LOG(rdInfoLog)
       << "********************************************************\n";
   BOOST_LOG(rdInfoLog) << "Testing R-Group Decomposition \n";
-
   testSymmetryMatching(FingerprintVariance);
   testSymmetryMatching();
   testRGroupOnlyMatching();
@@ -4210,6 +4239,7 @@ int main() {
   testStereoBondBug();
   testNotEnumeratedCore();
   testRgroupDecompZipping();
+  testSmartsOnDummyAtoms();
   BOOST_LOG(rdInfoLog)
       << "********************************************************\n";
   return 0;