Solution
I have finally gotten to post the results, written quite a while ago.
Thanks for all the suggestions.
The problem now is resolved. In fact the solution had been explicitly suggested on this forum, it was to use the fixboot command, which fixed it completely. I couldn't be sure of anything and had to make sense of things myself, which took somewhat longer, but in the end I could be confident I wouldn't damage anything else by trying to fix the problem. I wrote down some of my resolving steps below.
Freedos sys command seems to have replaced boot sector of the primary partition with other code. Now, absolute sector 63 had the following code, as copied down manually from the output of PTS disk editor available on the UBCD, since I couldn't save it to a file (no such option in the program):
0000 EB4C9000000000000000000002080000
0010 0000000000F800003F00FF003F000000
0020 0000000080008000ED1EBF0100000000
0030 000004000000000047CB080000006000
0040 00003F0000003F0000003F000000FAFC
0050 31CO8ED08EDBBDOO7C8D66EOFBB8ED01
0060 B106D3ED2DEDO78ECO89EE89EFB90001
0070 F3A506BB787C53CB8ED88ED0885624E8
0080 DD004C6F6164696E672046726565444F
0090 532E2E2E0D0A524F4F54DO8B46468B56
00A0 488B7E4031DB8E463EE8CF00723831FF
00B0 B90B00BEC77D57F3A65F268B451A740B
00C0 B3C72026803D0075E7726FE891002046
00D0 415400508E463E31DB8B7E168B46428B
00E0 5644E896005872521E061F07BF0040AD
00F0 89C601F601C6D1EEAD7304B104D3E880
0100 E40F3DFF0F72E831COAB0E1FE8500020
0110 4B45524E454C008E463E31DBBE0040AD
0120 09C0742948488B7E0D81E7FF00F7E703
0130 464A13564CE8430073E5E8FF00F7E703
0140 4F4F54206572726F722100EBFEE80F00
0150 20474F210D0A008A5E24EA0000600089
0160 76035E50535731DBB40EAC3C007404CD
0170 10EBF75F5B58568B7603C3565250F776
0180 1889D131D2F7761A88D6D0CCDOCC86C4
0190 8A561828CAFEC109C188D0B801028A56
01A0 24CD13730830E4CD13585AEBCF035E0B
01B0 73078CC080C4108EC0585A05010083D2
01C0 004F75B8F85ECB4345524E454C202053
01D0 59530000000000000000000000000000
01E0 00000000000000000000000000000000
01F0 000000000000000000000000000055AA
PTS disk editor allowed me to see that the message I was getting, "freedos root", was located in that sector, which can be seen by converting the above hex (unspaced ** values, for example EB4C9000 in the beginning, would look like EB 4C 90 00 in a hex editor) into ASCII. If spaced and without the offset markings, it should look like this:
EB 4C 90 00 00 00 00 00 00 00 00 00 02 08 00 00 00 00 00 00 00 F8 00 00 3F 00 FF 00 3F 00 00 00 00 00 00 00 80 00 80 00 ED 1E BF 01 00 00 00 00 00 00 04 00 00 00 00 00 47 CB 08 00 00 00 60 00 00 00 3F 00 00 00 3F 00 00 00 3F 00 00 00 FA FC 31 CO 8E D0 8E DB BD OO 7C 8D 66 EO FB B8 ED 01 B1 06 D3 ED 2D ED O7 8E CO 89 EE 89 EF B9 00 01 F3 A5 06 BB 78 7C 53 CB 8E D8 8E D0 88 56 24 E8 DD 00 4C 6F 61 64 69 6E 67 20 46 72 65 65 44 4F 53 2E 2E 2E 0D 0A 52 4F 4F 54 DO 8B 46 46 8B 56 48 8B 7E 40 31 DB 8E 46 3E E8 CF 00 72 38 31 FF B9 0B 00 BE C7 7D 57 F3 A6 5F 26 8B 45 1A 74 0B B3 C7 20 26 80 3D 00 75 E7 72 6F E8 91 00 20 46 41 54 00 50 8E 46 3E 31 DB 8B 7E 16 8B 46 42 8B 56 44 E8 96 00 58 72 52 1E 06 1F 07 BF 00 40 AD 89 C6 01 F6 01 C6 D1 EE AD 73 04 B1 04 D3 E8 80 E4 0F 3D FF 0F 72 E8 31 CO AB 0E 1F E8 50 00 20 4B 45 52 4E 45 4C 00 8E 46 3E 31 DB BE 00 40 AD 09 C0 74 29 48 48 8B 7E 0D 81 E7 FF 00 F7 E7 03 46 4A 13 56 4C E8 43 00 73 E5 E8 FF 00 F7 E7 03 4F 4F 54 20 65 72 72 6F 72 21 00 EB FE E8 0F 00 20 47 4F 21 0D 0A 00 8A 5E 24 EA 00 00 60 00 89 76 03 5E 50 53 57 31 DB B4 0E AC 3C 00 74 04 CD 10 EB F7 5F 5B 58 56 8B 76 03 C3 56 52 50 F7 76 18 89 D1 31 D2 F7 76 1A 88 D6 D0 CC DO CC 86 C4 8A 56 18 28 CA FE C1 09 C1 88 D0 B8 01 02 8A 56 24 CD 13 73 08 30 E4 CD 13 58 5A EB CF 03 5E 0B 73 07 8C C0 80 C4 10 8E C0 58 5A 05 01 00 83 D2 00 4F 75 B8 F8 5E CB 43 45 52 4E 45 4C 20 20 53 59 53 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 55 AA
I didn't want to further damage the computer this had occurred on, which has Windows XP as its os, so I tried to replicate the error on a Windows 98 computer. I inserted the floppy and used the "sys c:" command and almost as soon as it started I ejected the floppy, because that was how I remembered I did it, fearing the command would do something unwanted. This generated the same error message I was getting on the Windows XP computer, as expected and so I was now doing further testing on the Windows 98 computer.
Booting into the the recovery console (rc.iso) I used some command, prior to writing this, so I can't be sure which one of those offered in the post, (maybe fixboot) and it seems that command did just what I would've liked it to: booting into UBCD and using PTS disk editor I could now see different code in the primary partition boot sector(63). However this did not solve the problem as now instead of the "freedos root" message when booting from the hard drive I was getting a "Disk error Press any key to restart" message. This message as well could be found in the boot sector (63) just as the previous. Pressing any key did not cause the computer to restart but instead it made some noise (I suppose the computer tried interpreting the boot sector code but couldn't do that properly and instead of restarting read the boot sector again) and displayed the same message again. Pressing the key again would keep doing the same thing. But it could be that freedos sys command did not yet do anything besides writing the boot sector code. Maybe and probably the code I replaced it with using some command from the recovery console, was meant for Windows XP and therefore would not work for Windows 98. To check that I would have to try and find something that would put Windows 98 boot sector code back. If that solved the problem I could then simply use recovery console to replace the boot sector on the Windows XP computer. I then found out where there is a copy of the boot sector code (Windows 98SE Boot Sector), and after verifying that only sector 63 was different from what was supposed to be there, I copied the backup sector (69) using PTS disk editor after booting with UBCD, and pasted it into sector 63. The computer could now boot.