Unnecessary inserting entity after deleting it

[vitaliy-art]

Describe the bug
I described three entities, one of them is owned by others via @ManyToOne attribute. Then i create first entity, create second entity and create third entity, owned by first two. Then i delete first entity, update second entity and delete second entity. I expects that all entities is deleted from database, but before update second entity entity manager creates first entity again. And after all this steps i have in database first entity which was deleted.

Stack trace
There is no errors in stack trace.

To Reproduce
Steps to reproduce the behavior:

import { MikroORM, defineConfig } from '@mikro-orm/sqlite';
import { Entity, Property, PrimaryKey, ManyToOne, Cascade } from '@mikro-orm/core';

@Entity()
class Department {
    @PrimaryKey()
    public id!: number;

    @Property()
    public name!: string;
}

@Entity()
class Person {
    @PrimaryKey()
    public id!: number;

    @Property()
    public name!: string;
}

@Entity()
class Employee {
    @PrimaryKey()
    public id!: number;

    @ManyToOne({ onDelete: 'cascade' })
    public department!: Department;

    @ManyToOne({ onDelete: 'cascade' })
    public person!: Person;
}

(async () => {
    const config = defineConfig({
        entities: [Department, Person, Employee],
        dbName: 'db.bd',
        type: 'sqlite',
        allowGlobalContext: true,
        driverOptions: {
            'foreign_keys': 'ON',
        },
        debug: true,
    });

    const orm = await MikroORM.init(config);
    await orm.schema.updateSchema();
    const em = orm.em;

    const dep = new Department();
    dep.name = 'Department';
    await em.persistAndFlush(dep);

    const per = new Person();
    per.name = 'Person';
    await em.persistAndFlush(per);

    const emp = new Employee();
    emp.department = dep;
    emp.person = per;
    await em.persistAndFlush(emp);

    await em.removeAndFlush(dep);

    per.name = 'New Person';
    await em.persistAndFlush(per);
    await em.removeAndFlush(per);
    await orm.close();
})();

Starting log

Debugger attached.
[info] MikroORM version: 5.8.10
[discovery] ORM entity discovery started, using ReflectMetadataProvider
[discovery] - processing entity Department
[discovery] - processing entity Person
[discovery] - processing entity Employee
[discovery] - entity discovery finished, found 3 entities, took 19 ms
[info] MikroORM successfully connected to database db.bd
[query] select name as table_name from sqlite_master where type = 'table' and name != 'sqlite_sequence' and name != 'geometry_columns' and name != 'spatial_ref_sys' union all select name as table_name from sqlite_temp_master where type = 'table' order by name [took 8 ms, 0 result]
[query] pragma foreign_keys = off; [took 0 ms, 0 result]
[query] create table `department` (`id` integer not null primary key autoincrement, `name` text not null); [took 14 ms, 0 result]
[query] create table `person` (`id` integer not null primary key autoincrement, `name` text not null); [took 15 ms, 0 result]
[query] create table `employee` (`id` integer not null primary key autoincrement, `department_id` integer null, `person_id` integer null, constraint `employee_department_id_foreign` foreign key(`department_id`) references `department`(`id`) on delete cascade on update cascade, constraint `employee_person_id_foreign` foreign key(`person_id`) references `person`(`id`) on delete cascade on update cascade); [took 16 ms, 0 result]
[query] create index `employee_department_id_index` on `employee` (`department_id`); [took 16 ms, 0 result]
[query] create index `employee_person_id_index` on `employee` (`person_id`); [took 15 ms, 0 result]
[query] pragma foreign_keys = on; [took 0 ms, 0 result]

Expected log

[query] begin
[query] insert into `department` (`name`) values ('Department') returning `id` [took 8 ms]
[query] commit
[query] begin
[query] insert into `person` (`name`) values ('Person') returning `id` [took 7 ms]
[query] commit
[query] begin
[query] insert into `employee` (`department_id`, `person_id`) values (8, 8) returning `id` [took 11 ms]
[query] commit
[query] begin
[query] delete from `department` where `id` in (8) [took 12 ms]
[query] commit
[query] begin
[query] update `person` set `name` = 'New Person' where `id` = 8 [took 1 ms]
[query] commit
[query] begin
[query] delete from `person` where `id` in (8) [took 6 ms]
[query] commit
Debugger detached.

Actual log

[query] begin
[query] insert into `department` (`name`) values ('Department') returning `id` [took 7 ms]
[query] commit
[query] begin
[query] insert into `person` (`name`) values ('Person') returning `id` [took 10 ms]
[query] commit
[query] begin
[query] insert into `employee` (`department_id`, `person_id`) values (1, 1) returning `id` [took 11 ms]
[query] commit
[query] begin
[query] delete from `department` where `id` in (1) [took 9 ms]
[query] commit
[query] begin

> [query] insert into `department` (`id`, `name`) values (1, 'Department') returning `id` [took 6 ms]

[query] update `person` set `name` = 'New Person' where `id` = 1 [took 1 ms]
[query] commit
[query] begin
[query] delete from `person` where `id` in (1) [took 10 ms]
[query] commit
Debugger detached.

Versions

Dependency	Version
node	v20.6.1
typescript	5.2.2
mikro-orm	5.8.10
sqlite3	5.1.6