Problem with Schema Migration Overriding Indexes

I’m experiencing a serious issue with my MongoDB indexes getting overwritten while trying to integrate the new Schema Migration feature:

I understand that unique indexes are not supported yet, so I defined all of my indexes using MongoAltas including some unique and partial indexes as required.

However, when adding the schema option in my ParseServer class, all of those indexes are being overwritten and reset, even though my individual schemas do not include the indexes key, like so:

export const TestSchema = {
  className: 'Test',
  fields: {
    user: { type: 'Pointer', targetClass: '_User' },
    date: { type: 'String' },
    size: { type: 'Number' }
  classLevelPermissions: {
    find: { pointerFields: ['user'] },
    count: { pointerFields: ['user'] },
    get: { pointerFields: ['user'] },
    update: { pointerFields: ['user'] },
    delete: { pointerFields: ['user'] },
    create: {}

Is there a way where I can keep my cloud schema’s indexes intact while also using the schema migration feature?

Thanks in advance.