1985 Westfalia hightop with a manual transmission linked to a zero miles Ford Zetec Bostig conversion. (new engine, transmission rebuilt 32,000 miles ago)

If a transmission is sent in to have "limited slip" added, does the shop access all or just part of the transmission gearing system? 

 OR stated another way

Is there a logical reason that 4th gear would fail to stay engaged immediately after the transmission being worked on for the addition of a "peloquin" type unit?

Thanks in advance for any wisdom from those who know transmissions.