In the case where there are still Borrelia bacteria you're true, but if it can be checked that the intruders have vanished (which is the case in most cases of difficult to treat CLD or CF) then it should not pose any problem.

In the case where the Borrelia are just hiding and in a latent state, then all is a question of comparating the dynamics of the two sides: the time required by the Borrelia to wake up and proliferate, vs the time required by the vitamin D to reduce the autoimmunity to the point where the body is again desensitized about itself.

A short treatment of vitamin D would be sufficient to cure the immune problem and not long enough to allow the bacteria to take over. (Hypothetically. This is just a possibility and has to be researched, but this is exactly why I am enthusiastic.)

Also, contrary to steroidal treatment, vitamin D bolsters a part of the immunity (lymphocytes T), even if it dampens an other part. So, it would restore a balance which is lost in case of defective aquiered immunity.