Hey Jason -
Is the issue in identifying the current customers? Or is the issue in that they just don't care for the emails (ie they think they are SPAM)?
Customer marketing is always challenging - both in identifying customers and in tailoring information they care about when you deal with large customer bases. Depending on the goal(s) of the emails you send, you could always try multiple versions of the email based on customer segments in an effort to tailor a bit more (whether that's size, product, etc), and/or dive deeper into communication preference programs so that you remain relevant to customers.
If you can get the non-operational emails more segmented and relevant, you might see a decrease in operational emails that are reported as SPAM. To that point, what are your rules around how many times a customer can/should receive messages? And, how do you handle the number of marketing messages you send if you've seen an uptick in operational sends?
Lastly, perhaps try a different approach with operational sends - whether that's subject lines, from names or the general template. Something unique to let the customer know this is actually information that NEED to care about.
Just food for thought - and sorry if this is not even relevant to what you were asking!
-Ashleigh