I play Alpha Strike and choose my 4M unit, targeting four 1M units on the battlefield. My opponent reacts by playing Flash and moving two of those units to base. Considering rule 355.11, can I choose the subgroup that was moved to base as the resolution target for Alpha Strike?

No. Rule 355.11 only applies to cards whose targets must meet a group targeting requirement (like Fox-Fire's "total Might 4 or less"). Alpha Strike has no group requirement — each target must individually be "an enemy unit at a battlefield" (Rules 355.14.a, 355.10.b), so 355.11.b's subset re-selection never comes into play.

When Flash moves those two units to base, they stop meeting their individual targeting restriction. They remain "chosen" for counting effects like Repulse (FAQ #9921), but they are illegal targets for Alpha Strike's damage instruction, so they are unaffected at resolution (359.3.e.5). The instruction still executes on the targets that remain valid (359.3.e.8): your 4 damage is split only among the two units still at battlefields, each receiving at least 1 (355.14.g).