I have what I believe is Hardie siding, but it was installed over the old wood siding (previous owners). The old wood siding has rotted in various places at the bottom of the siding along the foundation. Since we have lived here we have installed new windows. My concern is that if the old wood siding that is rotting becomes a large enough problem that I need to remove it and redo the siding on the home, will the windows line up with the new siding since it won't be as thick? There is a trim along the windows so I assume the trim may just need to be thicker or doubled up. I also assume the windows could be uncaulked and whatnot and recessed into the home.

TLDR - Current siding installed over old wood siding. If all siding is removed and only one layer of siding is installed will it line up with windows? Will the window trim just need to be thicker? TIA

Smater, wiser minds than I may heve THE ANSWER
but thinking if rot is in your future, it well may be segregated to only the wet, grade area ... perhaps 12-24"high or less, hopefully.

Only that portion would need be repaired/replaced, even though both siding layers might be cut away and disposed. Look up the term wainscot and watertable, then consider what might replace the rotted skirt. Cultured.stone or stucco might be pricey but something no-rot (from the splashing) would be apropos here.

The above solution or just pull the bottom two layers of hardi remove rott and install siding and then hardi back

LP SmartSide trim