Why my product SEO URLs changed after Lightning install?

Lightning includes products links unification into shop.com/product-url form (with path of the deepest category displayed in breadcrumbs). With this search engines indexing becomes much faster and  number of pages to be cached reduces dramatically.

In general, there is no SEO sense to add category to product URL, it even hurts SEO a bit. This is done just to code breadcrumbs somewhere. Also the bad thing is that this way one product may have 3-6 different urls (one direct, one from manufacturer page, and one for each category it is listed at). This leads to much longer indexing times, bigger page caches and people get cached pages less often.

But you may disable this feature at Lightning Troubleshooting settings: