I trained my custom object detection with darknet yolov3 untill the average loss decreased down to 0.06 but now i want to train it with more training and test images (maybe also deleting some of the image files). Can I do these steps and continue to training with final .weights file or I should start it from the beginning?
Yes, you can use the currently trained model (.weights file) as the pre-trained model for the new training session. For example, if you use AlexeyAB repository you can train your model by a command like this:
darknet.exe detector train data/obj.data yolo-obj.cfg darknet53.conv.74
where darknet53.conv.74 is the pre-trained model.
In the new training session, you can add or remove images. However, the basic configurations should be correct (like the number of classes, etc).
According to the page I mentioned:
in the original repository original repository the weights-file is saved only once every 10 000 iterations