That is not a real problem.
Many apps handle this by checking for a prior version and giving a discount (see Omni or Affinity approach), by having an upgrade window (e.g. 1Password approach before switching to subs outside app store), or by just charging full freight again (which nobody who values software actually minds, and enterprises that budget full retail software per person/year anyway definitely don't even think about).
If you charge $X a month over time and think that's fair, you can charge $X * 24 every two years, and let people who dislike the upgrade treadmill just sit on the old version till iOS APIs shift out from under them.
In the meantime, you had the two years cash up front which funds future development.
> They get their licenses, I'm not getting my money because they just don't pay. Sucks to be me.
What are you talking about? The Apple Business Manager UI is a web based app store, one searches for the app, clicks to pay full retail, and you get your full money, immediately, the same as you get your IAP or sub. Meanwhile, the app is bought in bulk, assigned to the employee base, and you just sold 15,000 copies at retail by having a full price version when you otherwise couldn't sell any.
You don't talk to the enterprise and more importantly, I don't have to talk to you, or any other indie dev with weird bespoke purchasing processes not already approved by the enterprise procurement and expense systems.