I’ve been having these kinds of issues constantly, see for example this and this, and have not received much feedback from the insync people, despite sending the logs multiple times.
Lately, I realized insync do not re-activate (sync) after waking up from suspend, causing some issues. Imagine you work on folder X in your main computer while the laptop is suspended. You close the main computer and wake up the laptop. You see insync has the green tick, so you think all must be in sync. Then, you make some changes on folder X in the laptop, not realizing those are old versions. At that point, insync “wakes up” and realizes there are multiple versions of those files… creating the dreadful “(2)” copies.
Not sure if this is the culprit, but I’ve been avoiding suspending any of my two computers for a while, and always pausing and re-activating insync after waking up my laptop, and had no issues with duplicates since then. Hopefully the insync folks can check if this makes sense and release a fix…