TanyaYatskovska I did a lot of research before coming to this, it showed 2 things:
1. several threads for the same topic shows that many other people have faced similar issues
2. answer of Staff member in this thread leaves us with manually resolving conflicts
It is not a question of one issue, I think the part of how XML files are being modified when user makes changes on the GUI level needs significant improvement to eliminate or minimize unsolicited changes - like in the case when reordering one test suite or renaming one API triggers modifications in multiple files.
As for custom properties, having a flag for each property to mark it to persist or drop the value after execution could solve the issue of getting conflicts on dynamic properties, however saving current value somewhere for investigation purposes.
Without these changes it gets impractical to use ReadyAPI with a big team, which could force one to search for alternatives.