diff --git a/deploy/helm/sumologic/upgrade-2.0.0.sh b/deploy/helm/sumologic/upgrade-2.0.0.sh
index 4deb48acc3..7e908d8c5a 100755
--- a/deploy/helm/sumologic/upgrade-2.0.0.sh
+++ b/deploy/helm/sumologic/upgrade-2.0.0.sh
@@ -866,27 +866,28 @@ function migrate_fluent_bit() {
     else
       # Trim whitespace
       line="${line##+([[:space:]])}"
-
-      case "${SECTION}" in
-        "INPUT")
-          INPUTS="$(printf "%s\n  %s" "${INPUTS}" "${line}")"
-          ;;
-
-        "OUTPUT")
-          OUTPUTS="$(printf "%s\n  %s" "${OUTPUTS}" "${line}")"
-          ;;
-
-        "PARSER")
-          PARSERS="$(printf "%s\n  %s" "${PARSERS}" "${line}")"
-          ;;
-
-        "FILTER")
-          FILTERS="$(printf "%s\n  %s" "${FILTERS}" "${line}")"
-          ;;
-
-        *)
-          ;;
-      esac
+      if [[ -n "${line}" ]]; then
+        case "${SECTION}" in
+          "INPUT")
+            INPUTS="$(printf "%s\n  %s" "${INPUTS}" "${line}")"
+            ;;
+
+          "OUTPUT")
+            OUTPUTS="$(printf "%s\n  %s" "${OUTPUTS}" "${line}")"
+            ;;
+
+          "PARSER")
+            PARSERS="$(printf "%s\n  %s" "${PARSERS}" "${line}")"
+            ;;
+
+          "FILTER")
+            FILTERS="$(printf "%s\n  %s" "${FILTERS}" "${line}")"
+            ;;
+
+          *)
+            ;;
+        esac
+      fi
     fi
   done < <(echo "${RAWCONFIG}")
 
diff --git a/tests/upgrade_v2_script/static/fluent_bit.input.yaml b/tests/upgrade_v2_script/static/fluent_bit.input.yaml
index 2c85924236..7f24489dcd 100644
--- a/tests/upgrade_v2_script/static/fluent_bit.input.yaml
+++ b/tests/upgrade_v2_script/static/fluent_bit.input.yaml
@@ -53,6 +53,7 @@ fluent-bit:
         timeFormat: "%Y-%m-%dT%H:%M:%S.%L%z"
   rawConfig: |-
     @INCLUDE fluent-bit-service.conf
+
     [INPUT]
       Name             tail
       Path             /var/log/containers/*.log
@@ -65,10 +66,13 @@ fluent-bit:
       Skip_Long_Lines  On
       DB               /tail-db/tail-containers-state-sumo.db
       DB.Sync          Normal
+
     [OUTPUT]
       Name            test-output-1
+
     [FILTER]
       Name            test-filter-1
+
     [PARSER]
       Name            test-logfmt-parser-1
       Format          logfmt
@@ -130,4 +134,5 @@ fluent-bit:
       Systemd_Filter  _SYSTEMD_UNIT=var-lib-etcd2.service
       Max_Entries     1000
       Read_From_Tail  true
+
     @INCLUDE fluent-bit-output.conf