At some point in time, Calibre (currently at 5.10.1) stopped to retain empty lines in EPUB to FB2 conversion. Conversion options are:
Code:
{'asciiize': False,
'author_sort': None,
'authors': None,
'base_font_size': 0.0,
'book_producer': None,
'change_justification': 'original',
'chapter': "//*[((name()='h1' or name()='h2' or name()='h3' or name()='h4' or "
"name()='h5') and re:test(., "
"'\\s*((chapter|book|section|part)\\s+)|([IVX0-9]+\\.\\s+)|((prolog|prologue|epilogue)(\\s+|$))', "
"'i')) or @class = 'chapter']",
'chapter_mark': 'pagebreak',
'comments': None,
'cover': None,
'debug_pipeline': None,
'dehyphenate': True,
'delete_blank_paragraphs': True,
'disable_font_rescaling': False,
'duplicate_links_in_toc': False,
'embed_all_fonts': False,
'embed_font_family': None,
'enable_heuristics': False,
'expand_css': False,
'extra_css': None,
'fb2_genre': 'reference',
'filter_css': ',padding-top,background,background-color,padding-bottom,padding-right,padding-left,padding,color',
'fix_indents': True,
'font_size_mapping': None,
'format_scene_breaks': True,
'html_unwrap_factor': 0.4,
'input_encoding': None,
'input_profile': <calibre.customize.profiles.InputProfile object at 0x0584F2E0>,
'insert_blank_line': False,
'insert_blank_line_size': 0.5,
'insert_metadata': False,
'isbn': None,
'italicize_common_cases': True,
'keep_ligatures': False,
'language': None,
'level1_toc': None,
'level2_toc': None,
'level3_toc': None,
'line_height': 0.0,
'linearize_tables': False,
'margin_bottom': 5.0,
'margin_left': 5.0,
'margin_right': 5.0,
'margin_top': 5.0,
'markup_chapter_headings': True,
'max_toc_links': 50,
'minimum_line_height': 120.0,
'no_chapters_in_toc': False,
'no_inline_navbars': False,
'output_profile': <calibre.customize.profiles.GenericEink object at 0x0584F730>,
'page_breaks_before': '/',
'prefer_metadata_cover': False,
'pretty_print': False,
'pubdate': None,
'publisher': None,
'rating': None,
'remove_fake_margins': True,
'remove_first_image': False,
'remove_paragraph_spacing': False,
'remove_paragraph_spacing_indent_size': 1.5,
'renumber_headings': True,
'replace_scene_breaks': '',
'search_replace': '[]',
'sectionize': 'files',
'series': None,
'series_index': None,
'smarten_punctuation': True,
'sr1_replace': None,
'sr1_search': None,
'sr2_replace': None,
'sr2_search': None,
'sr3_replace': None,
'sr3_search': None,
'start_reading_at': None,
'subset_embedded_fonts': False,
'tags': None,
'timestamp': None,
'title': None,
'title_sort': None,
'toc_filter': None,
'toc_threshold': 6,
'transform_css_rules': '[]',
'unsmarten_punctuation': False,
'unwrap_lines': True,
'use_auto_toc': False,
'verbose': 2}