We know that pH affects the folding of proteins. Furthermore, normal lysosomal proteins have evolved structures that can survive and be active in the low pH conditions of the lysosome. Another possibility is the fusion protein is cleaved by a protease when it reaches the lysosome. In this scenario, the lysosomal protein segment of the fusion protein is inactive because the blood protein it is fused to inhibits its activity. The lysosomal protein might then become active if it could be released from the blood protein by a protease.
Lysosomes normally contain proteases.
So if these proteases are present in the lysosomes of the patients and if they are able to cleave the fusion proteins at appropriate sites, they may be able to activate the fusion proteins. Based on the fact that the compound being transported in a charged molecule, we can conclude that the molecule does not diffuse through the lipid portion of the membrane. So a transport protein must be involved. We haven't been told whether the transport process is active or passive. If it is passive, the most likely mechanism involves a membrane protein that binds the small compound within the lumen of the lysosome, undergoes a conformational change, and releases the compound in the cytoplasm.