I recently launched my SE save again, and got a pop-up message in the chat saying
"Rift Rail: Cybersyn compatibility data has been permanently removed from the save file."
I havent unlocked rift rails yet since i used the SE preset, but figured I should still ask why this is happening and if its going to be an issue later?

Hi! Thank you for reaching out. Please don't worry at all—this is completely normal and will NOT cause any issues with your save.
Here is what happened:
In a recent major update, I completely overhauled Rift Rail's underlying architecture. The old method used for Cybersyn compatibility was outdated, heavily reliant on workarounds, and could potentially impact performance. Because I want to keep the mod highly optimized, I entirely removed that legacy code.
The message you saw was just an automatic notification from my migration script, letting you know that it successfully ran a "housekeeping" routine to purge any obsolete background data, keeping your save file clean and lightweight.
Since you haven't even unlocked the portals yet, the script basically just deleted some empty tables in the background. When you eventually unlock and build the Rift Rails, everything will work perfectly using the new, optimized system.
Have fun with your Space Exploration run!