diff -ru a/src/document.c b/src/document.c
--- a/src/document.c	2019-01-04 18:26:24.000000000 +0300
+++ b/src/document.c	2019-02-23 00:58:33.019469539 +0300
@@ -2143,7 +2143,7 @@
 		editor_ensure_final_newline(doc->editor);
 	/* ensure newlines are consistent */
 	if (fp->ensure_convert_new_lines)
-		sci_convert_eols(doc->editor->sci, sci_get_eol_mode(doc->editor->sci));
+		editor_convert_eols(doc->editor);
 
 	/* notify plugins which may wish to modify the document before it's saved */
 	g_signal_emit_by_name(geany_object, "document-before-save", doc);
Only in b/src: document.c.orig
diff -ru a/src/editor.c b/src/editor.c
--- a/src/editor.c	2019-01-04 18:26:24.000000000 +0300
+++ b/src/editor.c	2019-02-23 00:58:33.020469540 +0300
@@ -4543,6 +4543,141 @@
 	}
 }
 
+struct Position
+{
+	gint pos;
+	gint virt;
+};
+
+struct Location
+{
+	gint line;
+	gint col;
+};
+
+struct Selection
+{
+	struct Location anchor;
+	struct Location caret;
+};
+
+struct Selections
+{
+	gint count;
+	struct Selection *array;
+};
+
+struct Location pos2loc(ScintillaObject *sci, struct Position const *pos)
+{
+	struct Location loc;
+	loc.line = sci_get_line_from_position(sci, pos->pos);
+	loc.col  = sci_get_column_from_position(sci, pos->pos) + pos->virt;
+	return loc;
+}
+
+struct Position loc2pos(ScintillaObject *sci, struct Location const *loc)
+{
+	struct Position pos;
+	pos.pos = sci_find_column(sci, loc->line, loc->col);
+	pos.virt = loc->col - sci_get_column_from_position(sci, pos.pos);
+	return pos;
+}
+
+struct Position get_anchor_pos(ScintillaObject *sci, gint i)
+{
+	struct Position pos;
+	pos.pos  = sci_get_selection_n_anchor(sci, i);
+	pos.virt = sci_get_selection_n_anchor_virtual_space(sci, i);
+	return pos;
+}
+
+void set_anchor_pos(ScintillaObject *sci, int i, struct Position const *pos)
+{
+	sci_set_selection_n_anchor(sci, i, pos->pos);
+	sci_set_selection_n_anchor_virtual_space(sci, i, pos->virt);
+};
+
+struct Location get_anchor_loc(ScintillaObject *sci, gint i)
+{
+	struct Position pos = get_anchor_pos(sci, i);
+	struct Location loc = pos2loc(sci, &pos);
+	return loc;
+}
+
+void set_anchor_loc(ScintillaObject *sci, gint i, struct Location const *loc)
+{
+	struct Position pos = loc2pos(sci, loc);
+	set_anchor_pos(sci, i, &pos);
+}
+
+struct Position get_caret_pos(ScintillaObject *sci, gint i)
+{
+	struct Position pos;
+	pos.pos  = sci_get_selection_n_caret(sci, i);
+	pos.virt = sci_get_selection_n_caret_virtual_space(sci, i);
+	return pos;
+}
+
+void set_caret_pos(ScintillaObject *sci, gint i, struct Position const *pos)
+{
+	sci_set_selection_n_caret(sci, i, pos->pos);
+	sci_set_selection_n_caret_virtual_space(sci, i, pos->virt);
+}
+
+struct Location get_caret_loc(ScintillaObject *sci, gint i)
+{
+	struct Position pos = get_caret_pos(sci, i);
+	struct Location loc = pos2loc(sci, &pos);
+	return loc;
+}
+
+void set_caret_loc(ScintillaObject *sci, gint i, struct Location const *loc)
+{
+	struct Position pos = loc2pos(sci, loc);
+	set_caret_pos(sci, i, &pos);
+}
+
+struct Selection get_selection_loc(ScintillaObject *sci, gint i)
+{
+	struct Selection sel;
+	sel.anchor = get_anchor_loc(sci, i);
+	sel.caret = get_caret_loc(sci, i);
+	return sel;
+}
+
+void set_selection_loc(ScintillaObject *sci, gint i, struct Selection const *sel)
+{
+	set_anchor_loc(sci, i, &sel->anchor);
+	set_caret_loc(sci, i, &sel->caret);
+}
+
+struct Selections get_selections_loc(ScintillaObject *sci)
+{
+	struct Selections sels = { 0, NULL };
+	gint mask = SCVS_RECTANGULARSELECTION | SCVS_USERACCESSIBLE;
+	if (sci_get_virtual_space_options(sci) & mask)
+	{
+		gint n = sci_get_selections(sci);
+		sels.array = g_malloc(n * sizeof(struct Selection));
+		for (gint i = 0; i < n; ++ i)
+		{
+			sels.array[ i ] = get_selection_loc(sci, i);
+		}
+		sels.count = n;
+	}
+	return sels;
+};
+
+void set_selections_loc(ScintillaObject *sci, struct Selections *sels)
+{
+	for (gint i = 0; i < sels->count; ++ i)
+	{
+		set_selection_loc(sci, i, &sels->array[i]);
+	}
+	sels->count = 0;
+	g_free(sels->array);
+	sels->array = NULL;
+}
 
 void editor_strip_trailing_spaces(GeanyEditor *editor, gboolean ignore_selection)
 {
@@ -4568,15 +4703,24 @@
 	}
 
 	sci_start_undo_action(editor->sci);
-
+	struct Selections sels = get_selections_loc(editor->sci);
 	for (line = start_line; line < end_line; line++)
 	{
 		editor_strip_line_trailing_spaces(editor, line);
 	}
+	set_selections_loc(editor->sci, &sels);
 	sci_end_undo_action(editor->sci);
 }
 
 
+void editor_convert_eols(GeanyEditor *editor)
+{
+	struct Selections sels = get_selections_loc(editor->sci);
+	sci_convert_eols(editor->sci, sci_get_eol_mode(editor->sci));
+	set_selections_loc(editor->sci, &sels);
+}
+
+
 void editor_ensure_final_newline(GeanyEditor *editor)
 {
 	gint max_lines = sci_get_line_count(editor->sci);
Only in b/src: editor.c.orig
diff -ru a/src/editor.h b/src/editor.h
--- a/src/editor.h	2019-01-04 18:26:24.000000000 +0300
+++ b/src/editor.h	2019-02-23 00:58:33.021469540 +0300
@@ -312,6 +312,8 @@
 
 void editor_strip_trailing_spaces(GeanyEditor *editor, gboolean ignore_selection);
 
+void editor_convert_eols(GeanyEditor *editor);
+
 void editor_ensure_final_newline(GeanyEditor *editor);
 
 void editor_insert_color(GeanyEditor *editor, const gchar *colour);