Troubleshooting a failing build (APK Signature Scheme v2 signer #1: APK integrity check failed. CHUNKED_SHA256 digest mismatch)

I did as instructed, but also noticed that when I had first built the APK from the terminal I forgot to run zipalign before signing it, which might have also been causing some problems.

That said, the build is still failing, but now at the v3 signer. I noticed the following outputs in the log file:

Verified using v1 scheme (JAR signing): true

Verified using v2 scheme (APK Signature Scheme v2): true

Verified using v3 scheme (APK Signature Scheme v3): true

Verified using v3.1 scheme (APK Signature Scheme v3.1): false

Verified using v4 scheme (APK Signature Scheme v4): false

Verified for SourceStamp: false

There are a number of warnings about various META-INF/* files not being protected by the signature and then the following error messages:

DOES NOT VERIFY

ERROR: APK Signature Scheme v3 signer #1: APK integrity check failed. CHUNKED_SHA256 digest mismatch. Expected: <1d39e4329acbd85e8f3030434ec87de3fd5ae06fa531afb522794e6f2295ad65>, actual: <7a5f9891f1ba5ecde290acc468e7147a2cf1a5ef3a65b5788d25dc9d09c32590>

2026-06-07 10:48:20,719 ERROR:

/tmp/tmpmkqg7yjj/sigcp_com.algol.obliquestrategies_1.apk:

2026-06-07 10:48:20,719 INFO: ...NOT verified - /tmp/tmpmkqg7yjj/sigcp_com.algol.obliquestrategies_1.apk

2026-06-07 10:48:21,022 DEBUG: > diff -r /tmp/tmpmkqg7yjj/tmp_binaries_com.algol.obliquestrategies_1.binary /tmp/tmpmkqg7yjj/_tmp_tmpmkqg7yjj_sigcp_com.algol.obliquestrategies_1

2026-06-07 10:48:21,224 WARNING: Keeping failed build "tmp/com.algol.obliquestrategies_1.apk"

2026-06-07 10:48:21,225 DEBUG: removing tmp/binaries/com.algol.obliquestrategies_1.binary.apk

2026-06-07 10:48:21,280 ERROR: Could not build app com.algol.obliquestrategies: compared built binary to supplied reference binary but failed

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verification of APK with copied signature failed

Comparing reference APK to APK with copied signature...

Unexpected diff output:

Binary files /tmp/tmpmkqg7yjj/tmp_binaries_com.algol.obliquestrategies_1.binary/content/assets/dexopt/baseline.prof and /tmp/tmpmkqg7yjj/_tmp_tmpmkqg7yjj_sigcp_com.algol.obliquestrategies_1/content/assets/dexopt/baseline.prof differ

Binary files /tmp/tmpmkqg7yjj/tmp_binaries_com.algol.obliquestrategies_1.binary/content/classes.dex and /tmp/tmpmkqg7yjj/_tmp_tmpmkqg7yjj_sigcp_com.algol.obliquestrategies_1/content/classes.dex differ

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Any ideas as to what might be happening?

Thank you