I realize I'm a little late to this party but I feel compelled to revive this. I have been repacking bsas for a while now, including vanilla and official DLCs, and I am really surprised to hear of others having so much trouble with it. Last time I played, I combined all vanilla, update, DG, HF, and DB into 5 (I think) bsas and played for around 100 hrs with no problems. At first I had to play around with settings and figure out what could or could not be compressed but I always use max compression and I have yet to have any problems with it. I also have not observed any difference between having those original flags set or not.
The only problem I have had with compression are sound files. Xwm files don't comress well so it doesn't make sense to try anyway. Wav files do compress well but the game either crashes or won't load them consistently. AFAICT, only sound fx must be wav.
BSAOpt can create mixed archives (meaning compress + uncomrpessed). Here is an example of what I do using Convenient Horses v5.0: Extract BSA (97.5MB)Convert all wavs in sound/voice to xwm
for /r %n in ("*.wav") do xwmaencode "%n" "%~pnn.xwm"(CD to the extraced files first! This command will recurse all folders under the currend directory!)Remove original wav files
for /r %n in ("*.xwm") do del "%~pnn.wav"(This will only delete a wav if there is an xwm with the same name.)Open BSAOpt, choose CH files and output bsa nameSet compression to maximumMake sure recursive is checked, select sound, uncheck allSelect scripts\source, uncheck allPackWhen done, choose root folder in top treeview, uncheck allChoose sound folder, check allSet compression to nonePack (49.1MB)I am currently trying to work up the motivation to write my own BSA packer. I want it to be a drop in replacement for archive.exe with more options e.g. choose compression and flag options before packing, 7-zip and zopfli compression algorithms, search for duplicates before adding to the archive, automatically create multiple archives if the archive becomes too large (IIRC, you can have 2GB + 1 file). I've been thinking about it for some time now but I only just started it and I tend to start projects that I never finish.
It may be specific to v2 but BSAOpt does set flags for me. For "Convenient Horses.bsa" the set flags are Meshes, Textures, Sounds, Voices, Shaders, and Misc.