It needs some @conflict/@pkgpath, I think it's something like this but
haven't checked carefully.

Index: Makefile
===================================================================
RCS file: /cvs/ports/mail/claws-mail/Makefile,v
retrieving revision 1.145
diff -u -p -r1.145 Makefile
--- Makefile	4 Feb 2024 14:35:21 -0000	1.145
+++ Makefile	11 Feb 2024 12:46:39 -0000
@@ -4,6 +4,7 @@ COMMENT-spamassassin=	spamassassin plugi
 COMMENT-pdfviewer=	pdfviewer plugin
 
 V=			4.2.0
+REVISION=		0
 DISTNAME=		claws-mail-${V}
 
 CATEGORIES=		mail news
@@ -18,7 +19,7 @@ SITES=			https://www.claws-mail.org/rele
 COMPILER =		base-clang ports-gcc base-gcc
 
 MULTI_PACKAGES=		-main -bogofilter -spamassassin -pdfviewer
-FLAVORS=		jpilot ldap
+FLAVORS=		ldap
 FLAVOR?=
 
 FLAVOR_STRING=		${FLAVOR_EXT:S/-/,/g}
@@ -87,6 +88,7 @@ LIB_DEPENDS-pdfviewer=	${LIB_DEPENDS} \
 CONFIGURE_ARGS+=	--disable-acpi_notifier-plugin \
 			--disable-compface \
 			--disable-fancy-plugin \
+			--disable-jpilot \
 			--disable-python-plugin \
 			--disable-tnef_parse-plugin \
 			--disable-bsfilter-plugin \
@@ -99,14 +101,6 @@ CONFIGURE_STYLE=	autoconf
 AUTOCONF_VERSION=	2.71
 CONFIGURE_ENV+=		CPPFLAGS="-I${X11BASE}/include" \
 			LDFLAGS="-L${X11BASE}/lib"
-
-.if ${FLAVOR:Mjpilot}
-LIB_DEPENDS-main+=	comms/pilot-link
-WANTLIB-main +=		pisock
-RUN_DEPENDS-main+=	comms/jpilot
-.else
-CONFIGURE_ARGS+=	--disable-jpilot
-.endif
 
 .if ${FLAVOR:Mldap}
 WANTLIB-main+=		lber ldap
Index: pkg/PLIST-bogofilter
===================================================================
RCS file: /cvs/ports/mail/claws-mail/pkg/PLIST-bogofilter,v
retrieving revision 1.8
diff -u -p -r1.8 PLIST-bogofilter
--- pkg/PLIST-bogofilter	11 Mar 2022 19:34:33 -0000	1.8
+++ pkg/PLIST-bogofilter	11 Feb 2024 12:46:39 -0000
@@ -1,4 +1,5 @@
 @pkgpath mail/sylpheed-claws,-bogofilter[,compface][,pgpmime][,jpilot][,ldap]
 @pkgpath mail/claws-mail,-bogofilter,compface${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-bogofilter,jpilot${FLAVOR_STRING}
 lib/claws-mail/plugins/bogofilter.la
 @so lib/claws-mail/plugins/bogofilter.so
Index: pkg/PLIST-main
===================================================================
RCS file: /cvs/ports/mail/claws-mail/pkg/PLIST-main,v
retrieving revision 1.48
diff -u -p -r1.48 PLIST-main
--- pkg/PLIST-main	4 Feb 2024 14:35:21 -0000	1.48
+++ pkg/PLIST-main	11 Feb 2024 12:46:39 -0000
@@ -1,14 +1,17 @@
+@conflict claws-mail-*-jpilot
 @conflict claws-mail-attremover-*
+@conflict claws-mail-gdata-*
 @conflict claws-mail-notification-*
 @conflict claws-mail-rssyl-*
 @conflict claws-mail-vcalendar-*
-@conflict claws-mail-gdata-*
-@pkgpath mail/claws-mail,-gdata[,compface]${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-gdata[,compface][,jpilot]${FLAVOR_STRING}
 @pkgpath mail/claws-mail-attremover
 @pkgpath mail/claws-mail-notification
 @pkgpath mail/claws-mail-rssyl
 @pkgpath mail/claws-mail-vcalendar
 @pkgpath mail/claws-mail,-main,compface${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-main,compface,jpilot${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-main,jpilot${FLAVOR_STRING}
 @pkgpath mail/sylpheed-claws,-main[,compface][,pgpmime][,jpilot][,ldap]
 @pkgpath mail/sylpheed-claws[,compface][,pgpmime][,jpilot][,ldap]
 @bin bin/claws-mail
Index: pkg/PLIST-pdfviewer
===================================================================
RCS file: /cvs/ports/mail/claws-mail/pkg/PLIST-pdfviewer,v
retrieving revision 1.4
diff -u -p -r1.4 PLIST-pdfviewer
--- pkg/PLIST-pdfviewer	11 Mar 2022 19:34:33 -0000	1.4
+++ pkg/PLIST-pdfviewer	11 Feb 2024 12:46:39 -0000
@@ -1,3 +1,4 @@
 @pkgpath mail/claws-mail,-pdfviewer,compface${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-pdfviewer,jpilot${FLAVOR_STRING}
 lib/claws-mail/plugins/pdf_viewer.la
 @so lib/claws-mail/plugins/pdf_viewer.so
Index: pkg/PLIST-spamassassin
===================================================================
RCS file: /cvs/ports/mail/claws-mail/pkg/PLIST-spamassassin,v
retrieving revision 1.8
diff -u -p -r1.8 PLIST-spamassassin
--- pkg/PLIST-spamassassin	11 Mar 2022 19:34:33 -0000	1.8
+++ pkg/PLIST-spamassassin	11 Feb 2024 12:46:39 -0000
@@ -1,4 +1,5 @@
 @pkgpath mail/sylpheed-claws,-spamassassin[,compface][,pgpmime][,jpilot][,ldap]
 @pkgpath mail/claws-mail,-spamassassin,compface${FLAVOR_STRING}
+@pkgpath mail/claws-mail,-spamassassin,jpilot${FLAVOR_STRING}
 lib/claws-mail/plugins/spamassassin.la
 @so lib/claws-mail/plugins/spamassassin.so