I gotta ask... Which software package are you using to program your 500? The reason I'm asking is that while I have both PSREdit500 and Win500 and have found that each one has enough `different quirks' as to how they handle different editing situations. (Though I will also admit that I don't do all that much `download' type of programming or editing preferring to picking up and using the .PDF and .CSV files and do `manual' entry/editing. [It allows me to arrange my "Primary" and "Secondary" control channels for each tower according to said tower's locations taking into account each one's `quirks' and locations re: Distance, obstructions, whether I'm listening from my base, or will be mobile, ETC..])
I also do a somewhat similar routine with the TGs though, sometimes that occurs more with `Scanlists' than with the control channels. (My PSR700s and PSR800s are the ones that really shine with their larger selection of `Scanlists'. {Wan Grin} when dealing with edited TGs but, if one doesn't have to deal with the `insanity' that occasionally rears it's `ugly head' with how things are setup here in Colo the PSR500/600 scanners can be `massaged' almost as well.
If one has already gotten a `good base' download then one can pretty much go ahead and go with using the data from either the .PDF or .CSV to `massage' or add any new or changed Control Channels / TalkGroups as necessary. (Also... one should probably always save the `updated' programming to a new `config' / `program' file to enable `backtracking' if necessary. [Another reason why I usually work with the .PDF/.CSV files for my `updates' (I also do pretty much the same with my PSR700s/PSR800s even though it is possible to let the software or radio apply `updates' because both have that somewhat `built-in'.)])
So... what you might try doing, if you can, is go back to a funtioning setup and then build up from there a piece at a time, if that change works, save it, and `play with it' to make certain it all still works then save it and move on to the next change. After you've done that for a while it'll become easier and you'll find that, except maybe for *major* changes, it's a lot faster and even more reliable than hoping whatever you may doesn't `mess things up at that one time you took the download for speed for speed's sake. Plus, it will help you develop a `familiarity' with the system and you will maybe even be able to `get a jump' on any new changes almost before they showup in either the .PDF/.CSV files or whatever maybe included in a download. (BTW, while it might seem to be a bit of an added expense to have up-to-date versions of the WIN500/PSRedit programs there are times when you may discover that one will do something you want done easier than the other. I've gotten so that I switch between programs without actually stopping to think about do it and now really cannot categorically say why I do it, I just do it. {VB GRIN!})