GPP doesn't specify if he is discussing fuel filler lines (hoses), vent lines, or fuel supply lines to the engines. I'd guess that they were still checking out all of the modifications required to fit the extra tanks, making sure that every component was working as-designed before they "covered" the lines.
Depending on which lines he is talking about, they could be covered for different reasons....insulation, protection from scooting about on top of the tanks, or just "house-keeping", if they are under-foot or might be encountered during regular maintenance.
We know three things about "covering the fuel lines" from Putnam's letter:
1. He calls the things to be covered "fuel lines."
2. Covering them requires "material" that did not arrive at Purdue in a timely fashion. In an October 24, 1936 letter to Mantz, GP wrote "I am terribly disappointed to find the material was so long delayed in reaching Bo at Lafayette. Apparently it got there only yesterday. This was a pretty tragic waist of time." It sounds to me like Mantz was responsible for getting the material shipped to Lafayette and Putnam is chewing him out.
3. He considers "covering the fuel lines" a high priority item.
We know from photos that the filling system for the fuselage tanks was changed several times. The first photo below was taken during the photo shoot on July 21. You can see that there were only two filler ports for the cabin tanks and one filler port for the two forward tanks.
The second photo was taken upon AE's arrival at Purdue on September 19, 1936. There are now at least three filler ports. Later, the third filler port visible in this photo was removed and covered with a patch. In the final iteration, there were four filler ports on the side of the fuselage and two on the top of the fuselage.
Bottom line: They had numerous problems with the fuel system and we're still trying to pin down exactly when the various changes were made.
Incidentally, our earlier speculation about the cockpit hatch being removed for the Purdue coed photos was apparently correct because Putnam's letter confirms that on November 14 the hatch had not yet been fixed.