diff --git a/src/curies/reconciliation.py b/src/curies/reconciliation.py
index 8484db6..ae55b25 100644
--- a/src/curies/reconciliation.py
+++ b/src/curies/reconciliation.py
@@ -4,6 +4,8 @@
 from collections import Counter, defaultdict
 from typing import Collection, List, Mapping, Optional, Tuple
 
+from typing_extensions import Literal
+
 from .api import Converter, Record
 
 __all__ = [
@@ -34,7 +36,12 @@ def __str__(self) -> str:
         )
 
 
-def remap_curie_prefixes(converter: Converter, remapping: Mapping[str, str]) -> Converter:
+def remap_curie_prefixes(
+    converter: Converter,
+    remapping: Mapping[str, str],
+    *,
+    intersection_resolution: Literal["overwrite", "drop"] = "drop",
+) -> Converter:
     """Apply CURIE prefix remappings.
 
     :param converter: A converter
@@ -68,9 +75,16 @@ def remap_curie_prefixes(converter: Converter, remapping: Mapping[str, str]) ->
                 new_record,
             )
         elif old in intersection:
-            record.prefix_synonyms = sorted(
-                set(record.prefix_synonyms).difference({old, new_prefix})
-            )
+            if intersection_resolution == "drop":
+                # throw away all synonyms from intersections,
+                # since there can be non-trivial overlaps
+                record.prefix_synonyms = []
+            elif intersection_resolution == "overwrite":
+                record.prefix_synonyms = sorted(
+                    set(record.prefix_synonyms).difference({old, new_prefix})
+                )
+            else:
+                raise TypeError(f"invalid intersection resolution mode: {intersection_resolution}")
             record.prefix = new_prefix
         else:
             record.prefix_synonyms = sorted(
diff --git a/tests/test_reconciliation.py b/tests/test_reconciliation.py
index d5c686a..013c4f1 100644
--- a/tests/test_reconciliation.py
+++ b/tests/test_reconciliation.py
@@ -77,6 +77,59 @@ def test_duplicate_correspondence(self):
         with self.assertRaises(InconsistentMapping):
             _order_curie_remapping(converter, curie_remapping)
 
+    def test_remapping_with_synonym(self):
+        """Test that remapping with synonym prefixes works as expected."""
+        r1 = Record(
+            prefix="geo",  # also should not survive
+            prefix_synonyms=["GEO", "should_not_survive"],
+            uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",
+            pattern="^G(PL|SM|SE|DS)\\d+$",
+        )
+        r2 = Record(
+            prefix="geogeo",
+            prefix_synonyms=["GEOGEO"],
+            uri_prefix="http://purl.obolibrary.org/obo/GEO_",
+            pattern="^\\d{9}$",
+        )
+        c1 = Converter([r1, r2])
+        remapping = {
+            "GEO": "ncbi.geo",
+            "geogeo": "GEO",
+        }
+        c2 = remap_curie_prefixes(c1, remapping)
+        r3 = Record(
+            prefix="ncbi.geo",
+            uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",
+            pattern="^G(PL|SM|SE|DS)\\d+$",
+        )
+        r4 = Record(
+            prefix="GEO",
+            prefix_synonyms=["GEOGEO", "geogeo"],
+            uri_prefix="http://purl.obolibrary.org/obo/GEO_",
+            pattern="^\\d{9}$",
+        )
+        self.assertEqual([r4, r3], c2.records)
+
+    def test_remapping_invalid_mode(self):
+        """Test that remapping with synonym prefixes works as expected."""
+        r1 = Record(
+            prefix="geo",  # also should not survive
+            prefix_synonyms=["GEO", "should_not_survive"],
+            uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",
+        )
+        r2 = Record(
+            prefix="geogeo",
+            prefix_synonyms=["GEOGEO"],
+            uri_prefix="http://purl.obolibrary.org/obo/GEO_",
+        )
+        c1 = Converter([r1, r2])
+        remapping = {
+            "GEO": "ncbi.geo",
+            "geogeo": "GEO",
+        }
+        with self.assertRaises(TypeError):
+            remap_curie_prefixes(c1, remapping, intersection_resolution="nope")
+
     def test_cycles(self):
         """Test detecting bad mapping with cycles."""
         converter = Converter(