You could do this in one query by building a composite query that combines the query that you would wish to execute against a specific index with a term or terms query that filters only to those indices you're interested in.
As an example, here's a query that executes a search request against all indices, but targets indices index-1 and index-2 differently to the rest by using two bool queries in the should clause of a bool query. Each of the inner bool queries combines a must clause (the query to execute) with a filter or must_not clause that determines the indices to apply to.
POST http://localhost:9200/_search
{
"query": {
"bool": {
"should": [
{
"bool": {
"must": [
{
"term": {
"query-field": {
"value": "query-term"
}
}
}
],
"filter": [
{
"terms": {
"_index": [
"index-1",
"index-2"
]
}
}
]
}
},
{
"bool": {
"must": [
{
"term": {
"no-match-query-field": {
"value": "no-match-query-term"
}
}
}
],
"must_not": [
{
"terms": {
"_index": [
"index-1",
"index-2"
]
}
}
]
}
}
]
}
}
}