### Godot version

master [4714e95896c8db02616ea6ec7f9aff92dec1cae4]

### System information

Godot v4.2.dev (4714e9589) - Ubuntu 20.04.6 LTS (Focal Fossa) - X11 - Vulkan (Forward+) - dedicated AMD Radeon RX 6800 XT - AMD Ryzen 9 5900X 12-Core Processor (24 Threads)

### Issue description

Sometimes when resizing the window on Linux X11 we may get the following validation error:

```
ERROR: VALIDATION - Message Id Number: -370888023 | Message Id Name: VUID-vkAcquireNextImageKHR-semaphore-01286
	Validation Error: [ VUID-vkAcquireNextImageKHR-semaphore-01286 ] Object 0: handle = 0xdcc8fd0000000012, type = VK_OBJECT_TYPE_SEMAPHORE; | MessageID = 0xe9e4b2a9 | vkAcquireNextImageKHR: Semaphore must not be currently signaled or in a wait state. The Vulkan spec states: If semaphore is not VK_NULL_HANDLE it must be unsignaled (https://vulkan.lunarg.com/doc/view/1.2.198.1/linux/1.2-extensions/vkspec.html#VUID-vkAcquireNextImageKHR-semaphore-01286)
```

I nailed down the problem. In `VulkanContext::prepare_buffers` we have the following loop (I simplified to highlight the problem):

```cpp
do {

err = fpAcquireNextImageKHR(device, w->swapchain, UINT64_MAX,
							w->image_acquired_semaphores[frame_index], VK_NULL_HANDLE, &w->current_buffer);

if (err == VK_SUBOPTIMAL_KHR) {
	// Swapchain is not as optimal as it could be, but the platform's
	// presentation engine will still present the image correctly.
	print_verbose("Vulkan: Early suboptimal swapchain, recreating.");
	Error swap_chain_err = _update_swap_chain(w);
	if (swap_chain_err == ERR_SKIP) {
		break;
	}
} while (err != VK_SUCCESS);
```

The problem is that vkAcquireNextImageKHR returned VK_SUBOPTIMAL_KHR but it already signaled the semaphore (because it is possible to continue normally with a VK_SUBOPTIMAL_KHR result).

Then we recreate the swapchain and reuse the w->image_acquired_semaphores[frame_index] which is in an inconsistent state.

I will handle this bug.

### Steps to reproduce

1. Open the Editor on any project
2. Resize the project until it happens

Reproducibility is much more frequent after applying PR #80566

### Minimal reproduction project

Any.
submit_info.waitSemaphoreCount = 0;
		submit_info.pWaitSemaphores = nullptr;
		submit_info.commandBufferCount = 1;
		submit_info.pCommandBuffers = command_buffer_queue.ptr();
		submit_info.signalSemaphoreCount = pending_flushable ? 1 : 0;
		submit_info.pSignalSemaphores = pending_flushable ? &draw_complete_semaphores[frame_index] : nullptr;
		VkResult err = vkQueueSubmit(graphics_queue, 1, &submit_info, VK_NULL_HANDLE);
		command_buffer_queue.write[0] = nullptr;
		ERR_FAIL_COND(err);
	}
	if (pending_flushable) {
		
		VkSubmitInfo submit_info;
		submit_info.sType = VK_STRUCTURE_TYPE_SUBMIT_INFO;
		submit_info.pNext = nullptr;
		VkPipelineStageFlags wait_stage_mask = VK_PIPELINE_STAGE_TOP_OF_PIPE_BIT;
		submit_info.pWaitDstStageMask = setup_flushable ? &wait_stage_mask : nullptr;
		submit_info.waitSemaphoreCount = setup_flushable ? 1 : 0;
		submit_info.pWaitSemaphores = setup_flushable ? &draw_complete_semaphores[frame_index] : nullptr;
		submit_info.commandBufferCount = command_buffer_count - 1;
		submit_info.pCommandBuffers = command_buffer_queue.ptr() + 1;
		submit_info.signalSemaphoreCount = 0;
		submit_info.pSignalSemaphores = nullptr;
		VkResult err = vkQueueSubmit(graphics_queue, 1, &submit_info, VK_NULL_HANDLE);
		command_buffer_count = 1;
		ERR_FAIL_COND(err);
	}
	vkDeviceWaitIdle(device);
}
Error VulkanContext::prepare_buffers() {