And the reason to NEVER top during your flowering process is because that's your main bud... You're just hurting your harvest, and the harvest of the most potent part of the plant, at that.... So yeah, leave the topping to veg!
But your plant will be fine... it just needs to rebuild its strength before coming back strong... a little stunted, but none the worse for wear...
However, you may have a bigger problem... Plants typically double and sometimes triple in size once they fully flower. If you're having space constraints now, that's not good... It's much better to prune and train early, with low potency smoke, than to harm your harvest by having to cull parts of the plant for size before they reach their peak... And unfortunately, the parts that are often culled are the most potent parts, like the top cola. So, it's definitely better to veg a smaller plant you never have to clip than to grow a monster you ruin by cutting for size... Just my opinion though.