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Judging from what you are telling, you haven't been flying Southwest for quite a while. Southwest's policy is that your miles expire after 24 months of inactivity. "Inactivity" in Southwest's terms is a little different from other airlines. While on United or American you can redeem miles once in a while and prolong your miles' existence, Southwest renders only miles accrual as an activity. More specifically, that is flying Southwest, obviously (paid flights, not reward flights), buying Rapid Rewards points, using a Southwest credit card, earning points from hotel and car partners that offer promotions or using a Rapid Rewards shopping portal.
There's a simple way around it: don't apply for co-branded credit cards. They are inconvenient in several different ways too. It's actually better to apply for regular travel credit cards. There are plenty of them now and the constant competition makes them set bigger bonuses and even better rewards programs. And the best part - miles and points never expire! If you've earned a large collection of miles on one card and then shoved it away somewhere and forgot about it entirely, you can just take it any time and redeem the miles you have.