G'Day Alex;
The paper says:
"Electro-magnetic Lorentz forces:
The authors of [394] considered the possibility that the Pioneer spacecraft can hold a charge and be deflected in its trajectory by Lorentz forces. They noted that this was a concern during planetary flybys due to the strength of Jupiter’s and Saturn’s magnetic fields (see Figure 2.1).
The magnetic field strength in the outer solar system, ≤ 10−5 Gauss, is five orders of magnitude smaller than the magnetic field strengths measured by the spacecraft at their nearest approaches to Jupiter: 0.185 Gauss for Pioneer 10 and 1.135 Gauss for Pioneer 11. Data from the Pioneer 10 plasma analyzer can be interpreted as placing an upper bound of 0.1μC on the positive charge during its Jupiter encounter [261].
These bounds allow us to estimate the upper limit of the contribution of the electromotive force on the motion of the Pioneer spacecraft in the outer solar system. This was accomplished in [18] using the standard formula for the Lorentz-force, F = qv × B, and found that the greatest force would be on Pioneer 11 during its closest approach to Jupiter, < 20 × 10−10 m/s2. However, once the spacecraft reached the interplanetary medium, this force would decrease to
σLorentz 2 × 10−14 m/s2, (5.7),
which is negligible."
Seems to me they have taken all that pretty well into account.
Welcome back !! We missed ya.

Cheers
PS:Both Pioneers had plasma analysers and instruments to measure the charge effect and that's where the above empirical data came from. Seems to be a big discrepency with "10^39 times stronger than gravity"....?