Hi @bijanstylez, welcome to the forum and thanks for your detailed post.
We’re not familiar with this exact behaviour in Logic, and our team regularly uses Scaler 3 with Logic in ongoing sessions without experiencing the issue you’ve described. Since you mentioned you’re on Scaler 3.1, could you update to the latest version which is v3.1.1 and let us know if the problem persists? This update includes a number of important fixes and stability improvements, including fixes related to project corruption across various DAWs.
If you still encounter the same issue in v3.1.1, please let us know - ideally with a video showing what’s happening. Cheers.