diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f62acb28432f347066e0089359ea2bb64a57fd5a..33092e163bfe1bf6c469244e2a634f15f5d82ff7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -211,17 +211,6 @@ stages:
     - if: $CI_PIPELINE_SOURCE == 'schedule'
       when: never
 
-# TODO: only temporary as long the MR encoder tests should not compare to main
-.rules-pytest-to-ref-enc-short-temp:
-  rules:
-    - if: $CI_PIPELINE_SOURCE == 'web' && $MANUAL_PIPELINE_TYPE == "pytest-compare"
-    - if: $CI_PIPELINE_SOURCE == 'push' && $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-    - if: $CI_PIPELINE_SOURCE == 'merge_request_event' && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "main" # only have MR pipelines for MRs to main
-    - if: $CI_PIPELINE_SOURCE == 'push'
-      when: never
-    - if: $CI_PIPELINE_SOURCE == 'schedule'
-      when: never
-
 .rules-pytest-to-main-short:
   rules:
     - if: $CI_PIPELINE_SOURCE == 'merge_request_event' && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "main" # only have MR pipelines for MRs to main
@@ -383,6 +372,7 @@ stages:
     IMAGES_ARTIFACT_NAME: "images_$CI_JOB_NAME"
     SUMMARY_HTML_ARTIFACT_NAME: "summary_$CI_JOB_NAME.html"
   script:
+    - set -euxo pipefail
     - *print-common-info
     - *update-scripts-repo
     - if [ $USE_LTV -eq 1 ]; then
@@ -430,7 +420,10 @@ stages:
     - diff_sba=0
     - diff_param=0
     - diff_report=0
-    - python3 scripts/batch_comp_audio.py --tool pyaudio3dtools -sd tests/dut/sba_bs/raw tests/dut_branch/sba_bs/raw || diff_sba=$?
+    # SHORT_TEST_SUITE_ENCODER does not contain test_sba.py. This leads to non-existing output folders being compared and to diff_sba=1. Therefore, this is skipped for the encoder tests
+    - if [ "$TEST_SUITE" != "$SHORT_TEST_SUITE_ENCODER" ]; then
+    -     python3 scripts/batch_comp_audio.py --tool pyaudio3dtools -sd tests/dut/sba_bs/raw tests/dut_branch/sba_bs/raw || diff_sba=$?
+    - fi
     - python3 scripts/batch_comp_audio.py --tool pyaudio3dtools -sd tests/dut/param_file/dec tests/dut_branch/param_file/dec || diff_param=$?
     - diff $CSV_BRANCH $CSV_MAIN || diff_report=$?
     - if [ $diff_param -eq 0 ] && [ $diff_sba -eq 0 ] && [ $diff_report -eq 0 ] && [ $zero_errors_branch -eq 1 ]; then
@@ -450,7 +443,7 @@ stages:
 
     - if [ $exit_code -eq 1 ]; then echo "Differences encountered"; exit_code=$EXIT_CODE_NON_BE; fi
     - if [ $zero_errors_branch != 1 ]; then echo "Run errors encountered!"; exit_code=$EXIT_CODE_NON_BE; fi
-    - if [ $regressions_found != 0 ]; then
+    - if [ $regressions_found != 0 ] && [ "$SKIP_REGRESSION_CHECK" != "true" ]; then
     -    if [ $allow_regressions_flag == 0 ]; then
     -        echo "Detected regression wrt to main, [allow regression] not set!"
     -        exit_code=$EXIT_CODE_FAIL;
@@ -727,39 +720,41 @@ build-codec-linux-debugging-make:
 # ---------------------------------------------------------------
 
 ### jobs that test fx encoder -> flt decoder
-# TODO: reenable once encoder tests shall compare to main
-# ivas-pytest-compare_to_main-short-enc:
-#   extends:
-#     - .rules-pytest-to-main-short
-#     - .test-job-linux
-#   before_script:
-#     - USE_LTV=0
-#     - DUT_DECODER_PATH=./IVAS_dec_ref
-#     - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
-#     - LEVEL_SCALING=1.0
-#   <<: *ivas-pytest-on-merge-request-anchor
-
-# ivas-pytest-compare_to_main-short-enc-lev-10:
-#   extends:
-#     - .rules-pytest-to-main-short
-#     - .test-job-linux
-#   before_script:
-#     - USE_LTV=0
-#     - DUT_DECODER_PATH=./IVAS_dec_ref
-#     - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
-#     - LEVEL_SCALING=0.3162
-#   <<: *ivas-pytest-on-merge-request-anchor
-
-# ivas-pytest-compare_to_main-short-enc-lev+10:
-#   extends:
-#     - .rules-pytest-to-main-short
-#     - .test-job-linux
-#   before_script:
-#     - USE_LTV=0
-#     - DUT_DECODER_PATH=./IVAS_dec_ref
-#     - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
-#     - LEVEL_SCALING=3.162
-#   <<: *ivas-pytest-on-merge-request-anchor
+ivas-pytest-compare_to_main-short-enc:
+  extends:
+    - .rules-pytest-to-main-short
+    - .test-job-linux
+  before_script:
+    - USE_LTV=0
+    - DUT_DECODER_PATH=./IVAS_dec_ref
+    - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
+    - LEVEL_SCALING=1.0
+    - SKIP_REGRESSION_CHECK="true"
+  <<: *ivas-pytest-on-merge-request-anchor
+
+ivas-pytest-compare_to_main-short-enc-lev-10:
+  extends:
+    - .rules-pytest-to-main-short
+    - .test-job-linux
+  before_script:
+    - USE_LTV=0
+    - DUT_DECODER_PATH=./IVAS_dec_ref
+    - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
+    - LEVEL_SCALING=0.3162
+    - SKIP_REGRESSION_CHECK="true"
+  <<: *ivas-pytest-on-merge-request-anchor
+
+ivas-pytest-compare_to_main-short-enc-lev+10:
+  extends:
+    - .rules-pytest-to-main-short
+    - .test-job-linux
+  before_script:
+    - USE_LTV=0
+    - DUT_DECODER_PATH=./IVAS_dec_ref
+    - TEST_SUITE="$SHORT_TEST_SUITE_ENCODER"
+    - LEVEL_SCALING=3.162
+    - SKIP_REGRESSION_CHECK="true"
+  <<: *ivas-pytest-on-merge-request-anchor
 
 ### jobs that test flt encoder -> fx decoder
 ivas-pytest-compare_to_main-short-dec:
@@ -805,8 +800,7 @@ ivas-pytest-compare_to_main-short-dec-lev+10:
 ### jobs that test fx encoder -> flt decoder
 ivas-pytest-compare_to_ref-short-enc:
   extends:
-    #- .rules-pytest-to-ref-short
-    - .rules-pytest-to-ref-enc-short-temp
+    - .rules-pytest-to-ref-short
     - .test-job-linux
   before_script:
     - USE_LTV=0
@@ -818,9 +812,8 @@ ivas-pytest-compare_to_ref-short-enc:
 
 ivas-pytest-compare_to_ref-short-enc-lev-10:
   extends:
-    #- .rules-pytest-to-ref-short
-    - .rules-pytest-to-ref-enc-short-temp
-    - .test-job-linux    
+    - .rules-pytest-to-ref-short
+    - .test-job-linux
   before_script:
     - USE_LTV=0
     - ENCODER_TEST="true"
@@ -831,9 +824,8 @@ ivas-pytest-compare_to_ref-short-enc-lev-10:
 
 ivas-pytest-compare_to_ref-short-enc-lev+10:
   extends:
-    #- .rules-pytest-to-ref-short
-    - .rules-pytest-to-ref-enc-short-temp
-    - .test-job-linux    
+    - .rules-pytest-to-ref-short
+    - .test-job-linux
   before_script:
     - USE_LTV=0
     - ENCODER_TEST="true"