QueryBuilder.withDeleted() position affects joined relations' soft delete filter

Issue description

When using QueryBuilder with .withDeleted() and join operations, the call position determines whether soft delete filters are applied to joined relations.

Expected Behavior

.withDeleted() should consistently include all soft-deleted records regardless of when it's called in the builder chain.

Actual Behavior

• withDeleted() BEFORE joins: All entities' soft delete filters removed ✅
• withDeleted() AFTER joins: Main entity's filter removed, but joined relations still filtered ❌

Steps to reproduce

Test Case 1: .withDeleted() AFTER joins (❌ INCORRECT)

  const recipients = await em
    .createQueryBuilder(Recipient, 'recipient')
    .leftJoinAndSelect('recipient.deal', 'deal')
    .leftJoinAndSelect('deal.contact', 'contact')
    .leftJoinAndSelect('deal.company', 'company')
    .where('recipient.team_id = :team_id', { team_id: 1 })
    .withDeleted()  // ← Position: AFTER joins
    .getMany();

Generated SQL (INCORRECT):

  // LEFT JOIN "deal" ON ... AND "deal"."deleted_at" IS NULL  ❌
  // LEFT JOIN "contact" ON ... AND "contact"."deleted_at" IS NULL  ❌
  // LEFT JOIN "company" ON ... AND "company"."deleted_at" IS NULL  ❌

Test Case 2: .withDeleted() BEFORE joins (✅ CORRECT)

  const recipients = await em
    .createQueryBuilder(Recipient, 'recipient')
    .withDeleted()  // ← Position: BEFORE joins
    .leftJoinAndSelect('recipient.deal', 'deal')
    .leftJoinAndSelect('deal.contact', 'contact')
    .leftJoinAndSelect('deal.company', 'company')
    .where('recipient.team_id = :team_id', { team_id: 1 })
    .getMany();

Generated SQL (CORRECT):

  // LEFT JOIN "deal" ON ...  ✅
  // LEFT JOIN "contact" ON ...  ✅
  // LEFT JOIN "company" ON ...  ✅

My Environment

Dependency	Version
Operating System	macOS
Node.js version	22.14.0
Typescript version	5.7.3
TypeORM version	0.3.21

Additional Context

No response

Relevant Database Driver(s)

• aurora-mysql
• aurora-postgres
• better-sqlite3
• cockroachdb
• cordova
• expo
• mongodb
• mysql
• nativescript
• oracle
• postgres
• react-native
• sap
• spanner
• sqlite
• sqlite-abstract
• sqljs
• sqlserver

Are you willing to resolve this issue by submitting a Pull Request?

Yes, I have the time, and I know how to start.

Start by reproducing the two createQueryBuilder chains using withDeleted(), leftJoinAndSelect(), and PostgreSQL, then compare the generated SQL for joined soft-delete filters. Done means withDeleted() removes the joined relations' soft-delete filters consistently regardless of whether it appears before or after the joins.