The error you're encountering, INSTALL_FAILED_INTERNAL_ERROR: Failed to extract native libraries, res=-110 and INSTALL_FAILED_INVALID_APK: Failed to extract native libraries, res=-2, is directly related to the alignment and structure of your modified config.arm64_v8a.apk. The key log line is:

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E NativeLibraryHelper: extractNativeLibs=false library 'libmegazord.so' is not PAGE(4096)-aligned within apk (APK alignment, not ELF alignment) - will not be able to open it directly from apk.

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Root Cause

1. APK Alignment Issue

• Android requires all APKs (including split APKs like config.arm64_v8a.apk) to be 4KB (4096-byte) aligned for native libraries (.so files) to be extracted and loaded correctly.
• Your zipalign -v 4 command aligns the APK, but if the native libraries inside the APK are not properly aligned or the APK itself is not correctly structured after modification, this error occurs.
• The log explicitly states that libmegazord.so is not page-aligned within the APK.

2. Split APK Structure

• When using install-multiple, all split APKs must be properly aligned and signed with the same key.
• If the base.apk and config.arm64_v8a.apk are not signed with the same key, or if the alignment is broken, the installer will fail.

3. Modification Impact

• Modifying files in config.arm64_v8a.apk (especially if it affects the lib/ directory or the APK's internal structure) can break the alignment or the expected layout.

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How to Fix

1. Recheck APK Alignment

• After rebuilding with apktool b, always run zipalign -v 4 on the output APK.
• Verify alignment with:

  bash
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  zipalign -c -v 4 config.arm64_v8a/dist/config.arm64_v8a_aligned.apk

  If this fails, re-align the APK.

2. Ensure Consistent Signing

• All split APKs (base.apk, config.arm64_v8a.apk, config.xxhdpi.apk) must be signed with the same key.
• Use the same keystore and alias for all APKs:

  bash
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  apksigner sign --ks mykey.jks --ks-key-alias myalias --out base_signed.apk base.apk
  apksigner sign --ks mykey.jks --ks-key-alias myalias --out config.arm64_v8a_signed.apk config.arm64_v8a/dist/config.arm64_v8a_aligned.apk
  apksigner sign --ks mykey.jks --ks-key-alias myalias --out config.xxhdpi_signed.apk config.xxhdpi.apk

• Then install with:

  bash
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  adb install-multiple base_signed.apk config.arm64_v8a_signed.apk config.xxhdpi_signed.apk

3. Check Native Library Alignment

• The error mentions libmegazord.so is not page-aligned within the APK.
• After rebuilding, ensure that the lib/ directory in the APK is correctly structured and that the .so files are not corrupted.
• You can inspect the APK contents with:

  bash
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  unzip -l config.arm64_v8a/dist/config.arm64_v8a_aligned.apk | grep lib/

  If the .so files are missing or misplaced, the rebuild process may have failed.

4. Rebuild with apktool Correctly

• When rebuilding with apktool b, use the --use-aapt2 flag (if available) for better compatibility:

  bash
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  apktool b --use-aapt2 config.arm64_v8a -o config.arm64_v8a_rebuilt.apk

• Then align and sign as above.

5. Verify APK Structure

• Use aapt or apktool to dump the APK and check for issues:

  bash
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  aapt dump badging config.arm64_v8a/dist/config.arm64_v8a_aligned.apk

  Look for warnings or errors.

6. Test with a Clean Rebuild

• Start fresh: decompress, modify, rebuild, align, and sign all split APKs again.
• Ensure no files are accidentally deleted or corrupted during modification.

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Summary of Commands

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# Rebuild
apktool b --use-aapt2 config.arm64_v8a -o config.arm64_v8a_rebuilt.apk

# Align
zipalign -v 4 config.arm64_v8a_rebuilt.apk config.arm64_v8a_aligned.apk

# Sign all split APKs with the same key
apksigner sign --ks mykey.jks --ks-key-alias myalias --out base_signed.apk base.apk
apksigner sign --ks mykey.jks --ks-key-alias myalias --out config.arm64_v8a_signed.apk config.arm64_v8a_aligned.apk
apksigner sign --ks mykey.jks --ks-key-alias myalias --out config.xxhdpi_signed.apk config.xxhdpi.apk

# Install
adb install-multiple base_signed.apk config.arm64_v8a_signed.apk config.xxhdpi_signed.apk

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If the Issue Persists

• The problem might be with the original APK structure or how apktool handles split APKs.
• Try using bundletool (for Android App Bundles) or manually repack the APKs with zip and signapk for more control.
• Alternatively, consider modifying the base.apk instead of the split APK, if possible.