What exactly are you talking about? Replacing the existing ships with capitol ships for what purpose? If its for random encounters, your better off using the tutorial reagarding that in this forum. If its something else, please specify.

No, I mean buying Capital ships or Cruisers from bases, after replacing them with existing ships for sale.

Its been done already. Under market ships, you'll find lists of ships sold. A sample of it looks like this.
[BaseGood
base = Br01_08_base <--area code
marketgood = gf1_package, 0, -1, 0, 0, 1, 1, 1
marketgood = gf2_package, 4, -1, 0, 0, 1, 1, 1
marketgood = gf4_package, 13, -1, 0, 0, 1, 1, 1
marketgood = gf5_package, 24, -1, 0, 0, 1, 1, 1
marketgood = gf6_package, 30, -1, 0, 0, 1, 1, 1
marketgood = bwf_package, 4, -1, 0, 0, 1, 1, 1
marketgood = bwe_package, 20, -1, 0, 0, 1, 1, 1
marketgood = bwe2_package, 30, -1, 0, 0, 1, 1, 1
marketgood = bwfr_package, 10, -1, 0, 0, 1, 1, 1
marketgood = cof_package, 8, -1, 1, 1, 0, 1, 1 <--this ship sold
marketgood = coe_package, 28, -1, 0, 0, 1, 1, 1
marketgood = coe2_package, 32, -1, 0, 0, 1, 1, 1
marketgood = lf_package, 1, -1, 0, 0, 1, 1, 1
marketgood = le_package, 2, -1, 0, 0, 1, 1, 1
marketgood = lfr_package, 1, -1, 0, 0, 1, 1, 1
marketgood = bf_package, 6, -1, 0, 0, 1, 1, 1
marketgood = be_package, 8, -1, 0, 0, 1, 1, 1
marketgood = bfr_package, 4, -1, 0, 0, 1, 1, 1
marketgood = kf_package, 10, -1, 0, 0, 1, 1, 1
marketgood = ke_package, 13, -1, 0, 0, 1, 1, 1
marketgood = kfr_package, 10, -1, 0, 0, 1, 1, 1
marketgood = rf_package, 20, -1, 0, 0, 1, 1, 1
marketgood = re_package, 22, -1, 0, 0, 1, 1, 1
marketgood = rfr_package, 20, -1, 0, 0, 1, 1, 1
marketgood = pf_package, 2, -1, 0, 0, 1, 1, 1
marketgood = pe_package, 13, -1, 0, 0, 1, 1, 1
marketgood = pfr_package, 4, -1, 0, 0, 1, 1, 1
marketgood = bhf_package, 4, -1, 0, 0, 1, 1, 1
marketgood = bhe_package, 13, -1, 0, 0, 1, 1, 1
marketgood = bhe2_package, 26, -1, 0, 0, 1, 1, 1
marketgood = oe_package, 16, -1, 0, 0, 1, 1, 1

Just follow the tutorials and look for whichever base sold ship you want to replace following the area code.

I mean I want to replace it with a capital ship, such as the Rheinland battleship or something.

Something perfect would be the Prison ship found in one of the earlier missions.

Is there any way whatsoever to replace existing (pilotable) ships in Freelancer to capital ships? Something along the lines of Wanderer's Liberty Battleship mod.

Umm do u mean by FLYING the cap ships? I didnt even know it was possible.
Hahah! That means I can fire the UBER STRONG cap lasers that blew up the other ships in 1 shot!!!

The final decision made by a single boy, the dark spirit of a past prince.