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The math IS changed in a number of respects, though most official Lancer modules shouldn't feel it too hard given the levels they tend to hover around. The biggest change is that a lot of NPCs had levels of excessive accuracy/to-hit numbers pared down, which will have an effect in terms of things like Evasion, cover, the Impaired condition, and Lock On all being more important and impactful in various ways.

The bigger changes will occur at higher levels of play, most notably Tier 3. At this level, a number of dangerous strikers have had their attacks shifted from multiple attacks per tier to single attacks with conventional damage scaling. In other words, instead of a Tier 3 Operator making three attacks for 7 damage every time they pull they trigger, they make one attack that deals 11 damage.

A lot of GMs are accustomed to accounting for these sorts of enemies at higher levels and their players are accustomed to facing them and so a lot of "metas" have developed around this. Using the rebake NPCs, this no longer really exists. At higher levels of play when using rebakes, the general advice I give is for GMs to utilize more templated NPCs (Veterans, Elites, etc) and/or simply more actual NPCs.

Most of the pre-written Lancer modules are designed to take place at lower levels, usually starting at LL0 and going out to maybe LL4 or so, so none of them should really require any extensive overhauling if using rebake NPCs. People have been running Solstice Rain and Winter Scar and Wallflower using them and it's worked fine. At higher levels is where things may need to adjust some.