The problem was that there was no ID clash or at least I couldnt see one. 0.47 detects a clash and renames the ID.
In the most recent file where it happened the icon had linearGradient3299 replaced with linearGradient3293 from the background's gradients.
In 0.47 linearGradient3299 becomes linearGradient3299-1 after the merge. There is no linearGradient3299 in the background or in the merged graphic.
The problem was that there was no ID clash or at least I couldnt see one. 0.47 detects a clash and renames the ID.
In the most recent file where it happened the icon had linearGradient3299 replaced with linearGradient3293 from the background's gradients.
In 0.47 linearGradient3299 becomes linearGradient3 299-1 after the merge. There is no linearGradient3299 in the background or in the merged graphic.