MySQL Index is bigger than the data stored

You can remove index A, because, as you have noted, it is a subset of another index. And it's possible to do this without disrupting normal processing.

The size of the index files is not alarming in itself and it can easily be true that the net benefit is positive. In other words, the usefulness and value of an index shouldn't be discounted because it results in a large file.

Index design is a complex and subtle art involving a deep understanding of the query optimizer explanations and extensive testing. But one common mistake is to include too few fields in an index in order to make it smaller. Another is to test indexes with insufficient, or insufficiently representative data.

I may be wrong, but the first index (idx_customer_invoice) is UNIQUE, the second (idx_customer_invoice_order) is not, so you'll probably lose the uniqueness constraint when you remove it. No?

Is there a way to find unused indexes in MySQL?

The database engine optimizer will select a proper index when attempting to optimize your query. Depending on when you collected statistics on your indexes last, the index which is chosen will vary. Unused indexes could suddenly become used because of new data repartition.

Can indexA safely be removed?

I would say yes, if indexA and indexB are B-Tree indexes. This is because an index that starts with the same columns in the same order will have the same structure.