While substituting lemons will not produce a strictly authentic Sopa de Lima, it is far from a culinary disaster. You can still create a very balanced and aromatic soup, provided you understand the differences in the citrus profiles and adjust your preparation accordingly.
Authentic Yucatecan Sopa de Lima is traditionally made with lima agria (bitter lime), a specific regional citrus that is floral, moderately acidic, and distinctively bitter. Outside of southeastern Mexico, standard Persian or Key limes are already an approximation. Lemons have a brighter, sweeter acidity and lack the musky, floral bitterness that defines Sopa de Lima. If you simply replace lime juice with lemon juice, the soup will lean slightly toward a Mediterranean or Greek lemon chicken soup, though your Mexican oregano, garlic, allspice, and charred peppers will keep the backbone firmly in Latin American territory.
If lemons are your only option today, you can get closer to the intended profile by using both lemon juice and finely grated zest, as the essential oils in the peel will provide that missing aromatic depth. If you happen to have an orange or a grapefruit, simmering a small piece of their peel in the broth alongside the lemon zest will also help mimic the complex floral bitterness of authentic Yucatecan limas.
Regarding freezing, citrus juice tends to lose its fresh top notes and can turn somewhat flat or unpleasantly bitter when frozen directly in a broth base for days or weeks. The best practice for freezing your meal prep is to freeze the spiced chicken broth without the citrus juice. When you are ready to reheat and serve a portion, bring the broth to a gentle simmer, remove it from the heat, and stir in your fresh lemon juice right at the end before adding your tortilla strips.
