In fact it depends on loco type. Pure DC or pure AC locomotives can switch the Main Switch on BEFORE raising pantographs. Moreover, you can´t do it other way, because electric layout do not allow you to raise pantos before you set Main Switch ON. Logically, if you switch OFF main Switch, any raised panto will be lowered. Bear in mind that these locos comes from 80´, when nobody has expected a train driver to be so dumb to raise pantos on one-system loco under different system that could damage it 
Some basic common inteligence has been predicted
On contrary, two-system locos (AC-DC) must raise pantos first - to detect type of current in catenary first and only after than you´re allowed to switch corresponding Main Switch.
About those neutral sections - when it comes to my E499.3, normal procedure should be to cut off any power the loco is taking from catenary, either it is traction force or EDB by setting "POMERNY TAH" (relative force) to zero. Then you can lower pantos with pantoswitch by setting it to 0, without switching Main Switch off. After passing you just raise pantos, wait for Ameter showing catenary voltage value and further proceed normally. If you lower your pantos while loco is still making any traction or electrodynamic braking force, you´ll end up with main switch of due to undervoltage protection.
Btw, this remainds me that I should translate some loco messages to english for foreign customers like yourself to understand what is happening with the loco itself in case some non-standard situation arise. Maybe in the next update
Thanks for your feedback, but I never noticed any significant FPS drop with my loco. I´ve tested it intensively, and compared to, say, Vectron from K-Trains it shines in FPS. Of course, due to extensive advanced scripting some FPS drops are present, but nothing heavy. Also I have compared it to few others from vR, RSSLO, even with DTG locos and haven´t noticed any big difference. Is everything ok on your side? Also depends on the route you play my loco on - it is well known that some czech routes are very expensive, when it comes to CPU power and require a decent machine to play it smoothly. If I may, I suggest to play ŽSR 150 from Simon Stehlík&Co or some parts of Podkrušnohorská Magistrála from Jirka Mrázek. Btw, E499.3009 was tested on these routes respectively.
For example, I play TSC on my notebook, that has Ryzen 7 5800H 3,2GHz, nVidia RTX 3060, 16GB RAM, Windows 10 Home and have on Jirka Mrazek´s routes cca. 40FPS. In TestovaciTrat I have almost 60FPS. Rain or snow does not make any difference, but of course, night setting do, especially when in stations with many lamps.
