i don't know, if you stop capture ,change filter to Ha ,focus again, and restart capturing ,would work..
1st,there is higly chance the software , to reject the new frames .
2nd,supposly you are capturing a nebula.How would you focus ,if there is no big star in the frame?
When i am focusing , i point to a big star, put my bahtinov mask on, change exposure time to 1 sec and binning 1 and then i focus.
Despite all, i will try your method ,if u try it 1st and works let me know please