diff --git a/src/mito2/src/compaction.rs b/src/mito2/src/compaction.rs
index 5cf3c444a8..73dfb5061c 100644
--- a/src/mito2/src/compaction.rs
+++ b/src/mito2/src/compaction.rs
@@ -1006,14 +1006,12 @@ impl CompactionSstReaderBuilder<'_> {
     /// for compaction. The schema of the [FlatSource] is unified.
     async fn build_flat_sst_reader(self) -> Result<FlatSource> {
         let scan_input = self.build_scan_input().await?.with_compaction(true);
-
-        let schema = scan_input.mapper.output_schema();
-        let schema = schema.arrow_schema();
+        let schema = scan_input.mapper.input_arrow_schema(true);
 
         let stream = SeqScan::new(scan_input)
             .build_flat_reader_for_compaction()
             .await?;
-        Ok(FlatSource::new_stream(schema.clone(), stream))
+        Ok(FlatSource::new_stream(schema, stream))
     }
 
     async fn build_scan_input(self) -> Result<ScanInput> {
@@ -1096,7 +1094,15 @@ impl CompactionSstReaderBuilder<'_> {
                 .map(|x| x.0.parquet_metadata())
             {
                 Ok(x) => x,
-                Err(e) if e.is_object_not_found() => continue,
+                Err(e) if e.is_object_not_found() => {
+                    warn!(
+                        e;
+                        "Input SST file does not exist during compaction metadata pre-read, skip it, region_id: {}, file: {}",
+                        file_handle.region_id(),
+                        file_handle.file_id()
+                    );
+                    continue;
+                }
                 Err(e) => return Err(e),
             };
             let file_metadata = parquet_metadata.file_metadata();
diff --git a/tests/cases/standalone/common/types/json/json2.result b/tests/cases/standalone/common/types/json/json2.result
index fdae802f3b..79526be76e 100644
--- a/tests/cases/standalone/common/types/json/json2.result
+++ b/tests/cases/standalone/common/types/json/json2.result
@@ -155,3 +155,60 @@ drop table json2_table;
 
 Affected Rows: 0
 
+create table json2_overlap (
+    ts timestamp time index,
+    j  json2
+) with (
+    'append_mode' = 'true',
+    'sst_format' = 'flat',
+);
+
+Affected Rows: 0
+
+insert into json2_overlap
+values (1, '{"a": {"b": 1}}'),
+       (3, '{"a": {"b": 3}}');
+
+Affected Rows: 2
+
+admin flush_table('json2_overlap');
+
++------------------------------------+
+| ADMIN flush_table('json2_overlap') |
++------------------------------------+
+| 0                                  |
++------------------------------------+
+
+insert into json2_overlap
+values (2, '{"a": {"b": "s2"}}'),
+       (4, '{"a": {"b": "s4"}}');
+
+Affected Rows: 2
+
+admin flush_table('json2_overlap');
+
++------------------------------------+
+| ADMIN flush_table('json2_overlap') |
++------------------------------------+
+| 0                                  |
++------------------------------------+
+
+admin compact_table('json2_overlap', 'swcs', '86400');
+
++-------------------------------------------------------+
+| ADMIN compact_table('json2_overlap', 'swcs', '86400') |
++-------------------------------------------------------+
+| 0                                                     |
++-------------------------------------------------------+
+
+select count(*) from json2_overlap;
+
++----------+
+| count(*) |
++----------+
+| 4        |
++----------+
+
+drop table json2_overlap;
+
+Affected Rows: 0
diff --git a/tests/cases/standalone/common/types/json/json2.sql b/tests/cases/standalone/common/types/json/json2.sql
index 57e113f8be..777f1e6b9e 100644
--- a/tests/cases/standalone/common/types/json/json2.sql
+++ b/tests/cases/standalone/common/types/json/json2.sql
@@ -47,3 +47,29 @@ select j.c, j.y from json2_table order by ts;
 select j.d from json2_table order by ts;
 
 drop table json2_table;
+
+create table json2_overlap (
+    ts timestamp time index,
+    j  json2
+) with (
+    'append_mode' = 'true',
+    'sst_format' = 'flat',
+);
+
+insert into json2_overlap
+values (1, '{"a": {"b": 1}}'),
+       (3, '{"a": {"b": 3}}');
+
+admin flush_table('json2_overlap');
+
+insert into json2_overlap
+values (2, '{"a": {"b": "s2"}}'),
+       (4, '{"a": {"b": "s4"}}');
+
+admin flush_table('json2_overlap');
+
+admin compact_table('json2_overlap', 'swcs', '86400');
+
+select count(*) from json2_overlap;
+
+drop table json2_overlap;