That's why it's failing. Try on customers.handle.keyword instead:
POST /my-alias-index/_update_by_query
{
"script": {
"source": "ctx._source['customers.company'] = params.company",
"lang": "painless",
"params": {
"company": "apple"
}
},
"query": {
"term": {
"customers.handle.keyword": "search-user815"
}
}
}