SoftLogix erases my I/O tree

is there a way to not have softlogix destroy all my I/O modules? I dont mind if it does, I just dont want to have to fix 1000 errors when this happens.

Explain in detail what "destroy all my I/O modules" means.

When you change controller families, like from CompactLogix to SoftLogix, the I/O tree necessarily has to get deleted. That's just the way the system works.

If you're having the whole I/O tree get spontaneously deleted from an RSLogix 5000 project, that's a different problem and you need to troubleshoot it in a step-by-step manner.