Dear ImGui doesn't attempt to create a swapchain for your main window.
The example code (main.cpp) in the Vulkan back-end calls a helper
ImGui_ImplVulkanH_CreateWindowSwapChain() which calls
vkCreateSwapchainKHR()... well, because it is an example app.. you should probably not call those helpers in those app, your app probably already creates a window and a swapchain.
When the multi-viewports feature enabled (only available in the 'docking' branch), it DOES create additional swap-chains for every secondary window it creates, those are not windows that you manage nor see at all so it shouldn't interferte with your window.
All the functions with the
ImGui_ImplVulkanH_ prefix are documented in imgui_impl_vulkan.h as serving two purposes: facilitating writing the demo app, and internally by the multi-viewports system. You shouldn't need to call those from your app and therefore there's should not be multiple swapchains trying to associate to a same window.