I was able to reproduce the bug. Just restart your kernel and evaluate the following commands exactly as they are (will take a minute or two). The problem seems to be related to my usage of the protected symbol E as a local variable in a Block because if I replace all ocurrences of E in the definition of fSailIntersection with, say F, I get correct results. FullSimplify seems to have some sort of cache where it stores previous results and this gets corrupted by the evaluation of the code below. Still a serious bug imo.
fOmega[d_] := If[MemberQ[{1, 2}, d], {0, Sqrt[d]}, {1/2, Sqrt[d]/2}];
fSailTestLessEqual[d_,S_,T_,{x_,y_}]:=Block[{},Off[N::meprec];Return[FullSimplify[(x((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2)+(S[[1]]+S[[2]]fOmega[d][[1]])(T[[1]]+T[[2]]fOmega[d][[1]])+S[[2]]T[[2]]fOmega[d][[2]]^2)^2+(y((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2)+(S[[1]]+S[[2]]fOmega[d][[1]])T[[2]]fOmega[d][[2]]-(T[[1]]+T[[2]]fOmega[d][[1]])S[[2]]fOmega[d][[2]])^2<=(S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2<=(x((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2)+(S[[1]]+S[[2]]fOmega[d][[1]])(T[[1]]+T[[2]]fOmega[d][[1]]+1)+S[[2]]T[[2]]fOmega[d][[2]]^2)^2+(y((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2)+(S[[1]]+S[[2]]fOmega[d][[1]])T[[2]]fOmega[d][[2]]-(T[[1]]+T[[2]]fOmega[d][[1]]+1)S[[2]]fOmega[d][[2]])^2&&-fOmega[d][[2]]/2<=S[[2]]fOmega[d][[2]]x+(S[[1]]+S[[2]]fOmega[d][[1]])y+T[[2]]fOmega[d][[2]]<=fOmega[d][[2]]/2]];On[N::meprec];];
fSailEdges[d_,S_,T_]:={(x-(-(S[[1]]+S[[2]]fOmega[d][[1]])(T[[1]]+T[[2]]fOmega[d][[1]])-S[[2]]T[[2]]fOmega[d][[2]]^2)/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2))^2+(y-(-(S[[1]]+S[[2]]fOmega[d][[1]])T[[2]]fOmega[d][[2]]+(T[[1]]+T[[2]]fOmega[d][[1]])S[[2]]fOmega[d][[2]])/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2))^2==1/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2),(x-(-(S[[1]]+S[[2]]fOmega[d][[1]])(T[[1]]+T[[2]]fOmega[d][[1]]+1)-S[[2]]T[[2]]fOmega[d][[2]]^2)/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2))^2+(y-(-(S[[1]]+S[[2]]fOmega[d][[1]])T[[2]]fOmega[d][[2]]+(T[[1]]+T[[2]]fOmega[d][[1]]+1)S[[2]]fOmega[d][[2]])/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2))^2==1/((S[[1]]+S[[2]]fOmega[d][[1]])^2+(S[[2]]fOmega[d][[2]])^2),-S[[2]]fOmega[d][[2]]x-(S[[1]]+S[[2]]fOmega[d][[1]])y-T[[2]]fOmega[d][[2]]==fOmega[d][[2]]/2,S[[2]]fOmega[d][[2]]x+(S[[1]]+S[[2]]fOmega[d][[1]])y+T[[2]]fOmega[d][[2]]==fOmega[d][[2]]/2};
fEqualities[d_,C_]:=Flatten[Table[Map[{{#[[1]],#[[1]]/.{Equal->Less}},{#[[2]],#[[2]]/.{Equal->GreaterEqual}},{#[[3]],#[[3]]/.{Equal->LessEqual}},{#[[4]],#[[4]]/.{Equal->Less}}}&,{fSailEdges[d,C[[i]],C[[Mod[i,Length[C]]+1]]]}][[1]],{i,1,Length[C]}],1];
fVerticesSelected[d_,C_]:=Block[{V,VT,VS,a,b},V=Select[fVertices[fEqualities[d,C]],Apply[And,Table[fSailTestLessEqual[d,C[[i]],C[[Mod[i,Length[C]]+1]],#[[1]]],{i,1,Length[C]}]]&];VT=DeleteDuplicates[Union[Map[#[[1]]&,V]],FullSimplify[#1==#2]&];VS=Table[{},{a,1,Length[VT]}];For[a=1,a<=Length[VT],{For[b=1,b<=Length[V],{If[FullSimplify[VT[[a]]==V[[b]][[1]]],VS[[a]]=Union[VS[[a]],V[[b]][[2;;3]]]],b++}],VS[[a]]=Sort[VS[[a]],MemberQ[{Less,Greater},Head[#1[[2]]]]&&MemberQ[{LessEqual,GreaterEqual},Head[#2[[2]]]]&],VS[[a]]=DeleteDuplicates[VS[[a]],FindInstance[Not[Implies[#1[[2]],#2[[2]]]],{x,y},Reals]==={}||FindInstance[Not[Implies[#2[[2]],#1[[2]]]],{x,y},Reals]==={}&],VS[[a]]={VT[[a]],VS[[a]]},a++}];Return[VS];];
fSailIntersection[d_,C_]:=Block[{a=0,V={},E={},P={},PF={},A={},S={},T=0,S2={},R={}},V=fVerticesSelected[d,C];E=Table[If[i!=j,Intersection[V[[i]][[2]],V[[j]][[2]]],{}],{i,1,Length[V]},{j,1,Length[V]}];If[Complement[Union[Flatten[Map[Length[#]&,E,{2}]]],{1,0}]==={},{P=Select[Position[Map[Length[#]==1&,E,{2}],True],#[[1]]<#[[2]]&];R=Table[{V[[P[[i]][[1]]]][[1]],V[[P[[i]][[2]]]][[1]],E[[P[[i]][[1]]]][[P[[i]][[2]]]][[1]][[2]]},{i,1,Length[P]}];}];Return[R];];
Z={{-5,0},{4,2},{-1,-3},{-2,3},{5,-1},{-4,-2},{1,3},{2,-3},{-4,1},{4,1},{-2,-3},{-1,3},{4,-2}};
ZI = fSailIntersection[2, Z]
ZI = fSailIntersection[2, Z]
fSailTestLessEqual[2,{-4,-2},{1,3},{5065/6232-(17 Sqrt[101/6])/1558,(12 Sqrt[2])/19-1/19 Sqrt[-206+570 (5065/6232-(17 Sqrt[101/6])/1558)-361 (5065/6232-(17 Sqrt[101/6])/1558)^2]}]
FullSimplify[24<=(-20+24 (5065/6232-(17 Sqrt[101/6])/1558))^2+(-8 Sqrt[2]+24 ((12 Sqrt[2])/19-1/19 Sqrt[-206+570 (5065/6232-(17 Sqrt[101/6])/1558)-361 (5065/6232-(17 Sqrt[101/6])/1558)^2]))^2]
Simplify[24<=(-20+24 (5065/6232-(17 Sqrt[101/6])/1558))^2+(-8 Sqrt[2]+24 ((12 Sqrt[2])/19-1/19 Sqrt[-206+570 (5065/6232-(17 Sqrt[101/6])/1558)-361 (5065/6232-(17 Sqrt[101/6])/1558)^2]))^2]
FullSimplify[5916+5 Sqrt[606]>=Sqrt[6 (5835701+9860 Sqrt[606])]]
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